Starting phenix.real_space_refine
on Wed Mar  4 22:17:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6iy3_9749/03_2026/6iy3_9749.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6iy3_9749/03_2026/6iy3_9749.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.67
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6iy3_9749/03_2026/6iy3_9749.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6iy3_9749/03_2026/6iy3_9749.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6iy3_9749/03_2026/6iy3_9749.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6iy3_9749/03_2026/6iy3_9749.cif"
  }
  resolution = 3.67
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.010
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     296      5.49       5
     S      27      5.16       5
     C    9834      2.51       5
     N    3167      2.21       5
     O    3749      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17073
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 825
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 859
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 5, 'TRANS': 105}
    Chain: "D"
      Number of atoms: 776
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 776
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 95}
    Chain: "E"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 708
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
    Chain: "G"
      Number of atoms: 841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 841
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 767
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
    Chain: "J"
      Number of atoms: 2972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2972
          Classifications: {'DNA': 147}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 146}
    Chain: "I"
      Number of atoms: 3056
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3056
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "O"
      Number of atoms: 4764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 580, 4764
          Classifications: {'peptide': 580}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 563}
          Chain breaks: 6
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "O"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.98, per 1000 atoms: 0.23
  Number of scatterers: 17073
  At special positions: 0
  Unit cell: (141.24, 130.68, 132, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P     296     15.00
     O    3749      8.00
     N    3167      7.00
     C    9834      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 523.6 milliseconds
  

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2590

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 11 sheets defined
      63.4% alpha, 2.8% beta
      108 base pairs and 268 stacking pairs defined.
    Time for finding SS restraints: 2.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.572A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.503A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 124
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    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
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 22
      removed outlier: 3.758A  pdb=" N   ALA G  21 " --> pdb=" O   ARG G  17 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLY G  22 " --> pdb=" O   SER G  18 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.526A  pdb=" N   ARG G  71 " --> pdb=" O   GLY G  67 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 56 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
    Processing helix  chain 'O' and resid 671 through 683
    Processing helix  chain 'O' and resid 684 through 689
    Processing helix  chain 'O' and resid 744 through 749
      removed outlier: 3.849A  pdb=" N   ALA O 748 " --> pdb=" O   TYR O 744 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 768 through 784
    Processing helix  chain 'O' and resid 797 through 812
      removed outlier: 3.510A  pdb=" N   GLN O 801 " --> pdb=" O   GLY O 797 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 827 through 839
      removed outlier: 3.693A  pdb=" N   ALA O 836 " --> pdb=" O   SER O 832 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 850 through 862
      removed outlier: 4.872A  pdb=" N   ALA O 856 " --> pdb=" O   ASN O 852 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   LYS O 857 " --> pdb=" O   GLU O 853 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 873 through 879
      removed outlier: 4.132A  pdb=" N   ILE O 877 " --> pdb=" O   PHE O 873 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 879 through 885
    Processing helix  chain 'O' and resid 895 through 900
      removed outlier: 4.017A  pdb=" N   MET O 899 " --> pdb=" O   GLU O 895 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 904 through 912
    Processing helix  chain 'O' and resid 933 through 938
    Processing helix  chain 'O' and resid 943 through 950
      removed outlier: 4.532A  pdb=" N   ASN O 947 " --> pdb=" O   PRO O 943 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 951 through 958
      removed outlier: 4.317A  pdb=" N   TRP O 955 " --> pdb=" O   SER O 951 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 976 through 987
    Processing helix  chain 'O' and resid 1021 through 1031
      removed outlier: 4.139A  pdb=" N   GLN O1025 " --> pdb=" O   ILE O1021 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   MET O1026 " --> pdb=" O   MET O1022 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1050 through 1061
      removed outlier: 3.904A  pdb=" N   GLN O1054 " --> pdb=" O   ASN O1050 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LYS O1056 " --> pdb=" O   ILE O1052 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LYS O1057 " --> pdb=" O   MET O1053 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ILE O1058 " --> pdb=" O   GLN O1054 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   CYS O1059 " --> pdb=" O   LEU O1055 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1068 through 1073
    Processing helix  chain 'O' and resid 1082 through 1085
      removed outlier: 3.770A  pdb=" N   VAL O1085 " --> pdb=" O   ILE O1082 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1082 through 1085'
    Processing helix  chain 'O' and resid 1086 through 1103
      removed outlier: 3.702A  pdb=" N   GLU O1090 " --> pdb=" O   ALA O1086 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LEU O1091 " --> pdb=" O   GLY O1087 " (cutoff:3.500A)
      Proline residue:  O1097  - end of helix
    Processing helix  chain 'O' and resid 1113 through 1126
    Processing helix  chain 'O' and resid 1139 through 1150
      removed outlier: 4.077A  pdb=" N   LEU O1146 " --> pdb=" O   ARG O1142 " (cutoff:3.500A)
      removed outlier: 5.192A  pdb=" N   ARG O1147 " --> pdb=" O   SER O1143 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   LEU O1148 " --> pdb=" O   GLU O1144 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1189 through 1194
    Processing helix  chain 'O' and resid 1194 through 1199
      removed outlier: 3.512A  pdb=" N   ARG O1199 " --> pdb=" O   ASP O1195 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1216 through 1228
      removed outlier: 4.062A  pdb=" N   VAL O1220 " --> pdb=" O   SER O1216 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1231 through 1243
      removed outlier: 3.818A  pdb=" N   VAL O1235 " --> pdb=" O   ILE O1231 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LYS O1240 " --> pdb=" O   ILE O1236 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   PHE O1241 " --> pdb=" O   GLN O1237 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1248 through 1263
      removed outlier: 4.801A  pdb=" N   LEU O1254 " --> pdb=" O   GLN O1250 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ALA O1260 " --> pdb=" O   SER O1256 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1264 through 1268
      removed outlier: 3.622A  pdb=" N   LYS O1267 " --> pdb=" O   ARG O1264 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1279 through 1288
      removed outlier: 3.681A  pdb=" N   ALA O1288 " --> pdb=" O   ASN O1284 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1290 through 1304
    Processing helix  chain 'O' and resid 1337 through 1344
      removed outlier: 3.907A  pdb=" N   GLU O1341 " --> pdb=" O   ARG O1337 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ALA O1344 " --> pdb=" O   SER O1340 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.854A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.887A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.595A  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 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'O' and resid 789 through 790
      removed outlier: 3.761A  pdb=" N   LEU O 790 " --> pdb=" O   ILE O 921 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'O' and resid 844 through 845
      removed outlier: 6.560A  pdb=" N   LEU O 820 " --> pdb=" O   ILE O 892 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'O' and resid 1007 through 1008
      removed outlier: 6.609A  pdb=" N   VAL O1007 " --> pdb=" O   ILE O1208 " (cutoff:3.500A)
      removed outlier: 8.045A  pdb=" N   ARG O1210 " --> pdb=" O   VAL O1007 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   VAL O1178 " --> pdb=" O   LEU O1209 " (cutoff:3.500A)

    581 hydrogen bonds defined for protein.
    1728 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      270 hydrogen bonds
      540 hydrogen bond angles
      0 basepair planarities
      108 basepair parallelities
      268 stacking parallelities
  Total time for adding SS restraints: 4.30

  Time building geometry restraints manager: 2.00 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: 3068
        1.33 -     1.45: 5432
        1.45 -     1.57: 8824
        1.57 -     1.68: 589
        1.68 -     1.80: 51
  Bond restraints: 17964
  Sorted by residual:
  bond pdb=" C3'  DC I  13 "
       pdb=" O3'  DC I  13 "
    ideal  model  delta    sigma   weight residual
    1.422  1.489 -0.067 3.00e-02 1.11e+03 5.02e+00
  bond pdb=" CB  VAL G 100 "
       pdb=" CG1 VAL G 100 "
    ideal  model  delta    sigma   weight residual
    1.521  1.451  0.070 3.30e-02 9.18e+02 4.51e+00
  bond pdb=" CB  PRO F  32 "
       pdb=" CG  PRO F  32 "
    ideal  model  delta    sigma   weight residual
    1.492  1.392  0.100 5.00e-02 4.00e+02 4.01e+00
  bond pdb=" C2'  DC I  58 "
       pdb=" C1'  DC I  58 "
    ideal  model  delta    sigma   weight residual
    1.525  1.488  0.037 2.00e-02 2.50e+03 3.40e+00
  bond pdb=" C3'  DC I  23 "
       pdb=" O3'  DC I  23 "
    ideal  model  delta    sigma   weight residual
    1.422  1.475 -0.053 3.00e-02 1.11e+03 3.18e+00
  ... (remaining 17959 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 24661
        2.65 -     5.30: 750
        5.30 -     7.96: 66
        7.96 -    10.61: 12
       10.61 -    13.26: 1
  Bond angle restraints: 25490
  Sorted by residual:
  angle pdb=" N   PRO O 959 "
        pdb=" CA  PRO O 959 "
        pdb=" CB  PRO O 959 "
      ideal   model   delta    sigma   weight residual
     103.25  109.92   -6.67 1.05e+00 9.07e-01 4.03e+01
  angle pdb=" C   ASN O1049 "
        pdb=" N   ASN O1050 "
        pdb=" CA  ASN O1050 "
      ideal   model   delta    sigma   weight residual
     121.54  130.81   -9.27 1.91e+00 2.74e-01 2.36e+01
  angle pdb=" C3'  DG J 109 "
        pdb=" C2'  DG J 109 "
        pdb=" C1'  DG J 109 "
      ideal   model   delta    sigma   weight residual
     101.60   95.31    6.29 1.50e+00 4.44e-01 1.76e+01
  angle pdb=" C3'  DC I  24 "
        pdb=" C2'  DC I  24 "
        pdb=" C1'  DC I  24 "
      ideal   model   delta    sigma   weight residual
     101.60   95.80    5.80 1.50e+00 4.44e-01 1.50e+01
  angle pdb=" C   THR F  30 "
        pdb=" N   LYS F  31 "
        pdb=" CA  LYS F  31 "
      ideal   model   delta    sigma   weight residual
     120.26  125.43   -5.17 1.34e+00 5.57e-01 1.49e+01
  ... (remaining 25485 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.96: 8500
       34.96 -    69.92: 1570
       69.92 -   104.88: 65
      104.88 -   139.84: 4
      139.84 -   174.80: 3
  Dihedral angle restraints: 10142
    sinusoidal: 6156
      harmonic: 3986
  Sorted by residual:
  dihedral pdb=" CA  PRO O 932 "
           pdb=" C   PRO O 932 "
           pdb=" N   GLU O 933 "
           pdb=" CA  GLU O 933 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.93  -37.07     0      5.00e+00 4.00e-02 5.50e+01
  dihedral pdb=" O2A ADP O2000 "
           pdb=" O3A ADP O2000 "
           pdb=" PA  ADP O2000 "
           pdb=" PB  ADP O2000 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  131.19  168.81     1      2.00e+01 2.50e-03 4.75e+01
  dihedral pdb=" C5' ADP O2000 "
           pdb=" O5' ADP O2000 "
           pdb=" PA  ADP O2000 "
           pdb=" O2A ADP O2000 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   83.52 -143.52     1      2.00e+01 2.50e-03 4.33e+01
  ... (remaining 10139 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 2076
       0.061 -    0.122: 682
       0.122 -    0.183: 118
       0.183 -    0.243: 12
       0.243 -    0.304: 4
  Chirality restraints: 2892
  Sorted by residual:
  chirality pdb=" CA  ASN O1050 "
            pdb=" N   ASN O1050 "
            pdb=" C   ASN O1050 "
            pdb=" CB  ASN O1050 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" CB  ILE D  54 "
            pdb=" CA  ILE D  54 "
            pdb=" CG1 ILE D  54 "
            pdb=" CG2 ILE D  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" C1'  DC I  24 "
            pdb=" O4'  DC I  24 "
            pdb=" C2'  DC I  24 "
            pdb=" N1   DC I  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.20    0.27 2.00e-01 2.50e+01 1.83e+00
  ... (remaining 2889 not shown)

  Planarity restraints: 2204
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT J 122 "   -0.039 2.00e-02 2.50e+03   1.88e-02 8.82e+00
        pdb=" N1   DT J 122 "    0.029 2.00e-02 2.50e+03
        pdb=" C2   DT J 122 "    0.014 2.00e-02 2.50e+03
        pdb=" O2   DT J 122 "    0.009 2.00e-02 2.50e+03
        pdb=" N3   DT J 122 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DT J 122 "   -0.025 2.00e-02 2.50e+03
        pdb=" O4   DT J 122 "   -0.009 2.00e-02 2.50e+03
        pdb=" C5   DT J 122 "   -0.003 2.00e-02 2.50e+03
        pdb=" C7   DT J 122 "    0.012 2.00e-02 2.50e+03
        pdb=" C6   DT J 122 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU H 102 "   -0.047 5.00e-02 4.00e+02   7.16e-02 8.20e+00
        pdb=" N   PRO H 103 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO H 103 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO H 103 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE O 946 "    0.021 2.00e-02 2.50e+03   1.90e-02 6.33e+00
        pdb=" CG  PHE O 946 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD1 PHE O 946 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE O 946 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE O 946 "    0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE O 946 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE O 946 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 2201 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 3677
        2.79 -     3.32: 14928
        3.32 -     3.84: 32019
        3.84 -     4.37: 36802
        4.37 -     4.90: 54368
  Nonbonded interactions: 141794
  Sorted by model distance:
  nonbonded pdb=" OP1  DC J  95 "
            pdb=" OG  SER O 904 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" NE2 GLN O1111 "
            pdb=" OD1 ASP O1184 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" OD2 ASP D  68 "
            pdb=" OH  TYR F  98 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH2 ARG A 131 "
     model   vdw
     2.303 3.120
  ... (remaining 141789 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 37 through 135)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 20 through 102)
}
ncs_group {
  reference = (chain 'C' and resid 11 through 117)
  selection = (chain 'G' and resid 11 through 117)
}
ncs_group {
  reference = (chain 'D' and resid 29 through 125)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     19.150
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
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      :  0.009   0.100  17964  Z= 0.391
  Angle     :  1.078  13.260  25490  Z= 0.611
  Chirality :  0.060   0.304   2892
  Planarity :  0.007   0.072   2204
  Dihedral  : 26.116 174.797   7552
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  8.24 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  2.04 %
    Favored  : 97.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.98 (0.17), residues: 1335
  helix: -2.21 (0.13), residues: 782
  sheet: -3.27 (0.48), residues: 72
  loop : -3.03 (0.23), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG O 854 
 TYR   0.027   0.004   TYR B  51 
 PHE   0.044   0.005   PHE O 946 
 TRP   0.018   0.003   TRP O1083 
 HIS   0.015   0.003   HIS O 984 

Details of bonding type rmsd
  covalent geometry    : bond        0.00906 (17964)
  covalent geometry    : angle       1.07832 (25490)
  hydrogen bonds       : bond        0.14767 (  851)
  hydrogen bonds       : angle       6.74818 ( 2268)

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

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

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 290
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.8545 (p) cc_final: 0.8171 (t)
REVERT: A  120 MET cc_start: 0.8067 (mtp) cc_final: 0.7802 (mtp)
REVERT: C   15 LYS cc_start: 0.8666 (mmtp) cc_final: 0.8377 (mttm)
REVERT: D   59 MET cc_start: 0.8721 (tpp) cc_final: 0.8334 (tpp)
REVERT: E  108 ASN cc_start: 0.8783 (t0) cc_final: 0.8559 (t0)
REVERT: E  133 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7509 (mt-10)
REVERT: G   77 ARG cc_start: 0.8317 (ttm170) cc_final: 0.8110 (ttm-80)
REVERT: O  933 GLU cc_start: 0.6393 (tp30) cc_final: 0.5535 (tp30)
REVERT: O 1124 ARG cc_start: 0.7370 (mmm160) cc_final: 0.7075 (ptp-110)
REVERT: O 1182 ASP cc_start: 0.7276 (p0) cc_final: 0.7005 (p0)
REVERT: O 1266 LYS cc_start: 0.6543 (mttt) cc_final: 0.6002 (tptp)
REVERT: O 1267 LYS cc_start: 0.7480 (mttt) cc_final: 0.6708 (tptt)
REVERT: O 1287 LEU cc_start: 0.7373 (pp) cc_final: 0.7148 (pp)
REVERT: O 1294 MET cc_start: 0.6690 (mmm) cc_final: 0.6314 (mmm)
  outliers start: 5
  outliers final: 2
  residues processed: 293
  average time/residue: 0.2150
  time to fit residues: 83.4175
Evaluate side-chains
  183 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 181
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  893 ILE
Chi-restraints excluded: chain O residue  931 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    7.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:    4.9990
   chunk 149 optimal weight:    8.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
C  31 HIS
D  47 GLN
D  82 HIS
D  84 ASN
E  68 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  38 ASN
H  49 HIS
H  95 GLN
O 685 GLN
O 776 GLN
** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 858 GLN
** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O1347 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.138080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.100112 restraints weight = 36243.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.099149 restraints weight = 38439.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.099935 restraints weight = 33321.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.100346 restraints weight = 26600.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.100471 restraints weight = 24667.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  17964  Z= 0.279
  Angle     :  0.770  12.032  25490  Z= 0.429
  Chirality :  0.044   0.190   2892
  Planarity :  0.006   0.056   2204
  Dihedral  : 30.707 177.625   4735
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.27 %
    Favored  : 92.73 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  8.33 %
    Favored  : 89.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.21), residues: 1335
  helix: -0.42 (0.17), residues: 823
  sheet: -3.13 (0.50), residues: 72
  loop : -2.69 (0.26), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E  72 
 TYR   0.017   0.002   TYR B  98 
 PHE   0.033   0.003   PHE O 946 
 TRP   0.037   0.003   TRP O1083 
 HIS   0.008   0.002   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00637 (17964)
  covalent geometry    : angle       0.77000 (25490)
  hydrogen bonds       : bond        0.06114 (  851)
  hydrogen bonds       : angle       4.71656 ( 2268)

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

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

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 198
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7732 (mmm-85)
REVERT: A   87 SER cc_start: 0.8631 (p) cc_final: 0.8381 (t)
REVERT: A   94 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7236 (mm-30)
REVERT: A  120 MET cc_start: 0.8192 (mtp) cc_final: 0.7891 (ttm)
REVERT: C   15 LYS cc_start: 0.8679 (mmtp) cc_final: 0.8360 (mtmm)
REVERT: D   42 TYR cc_start: 0.8040 (t80) cc_final: 0.7218 (t80)
REVERT: D   59 MET cc_start: 0.8623 (tpp) cc_final: 0.8367 (tpp)
REVERT: E   41 TYR cc_start: 0.8040 (m-80) cc_final: 0.7782 (m-80)
REVERT: F   92 ARG cc_start: 0.8668 (ptm-80) cc_final: 0.8405 (ptm-80)
REVERT: G   71 ARG cc_start: 0.7978 (mtp-110) cc_final: 0.7739 (ptp-170)
REVERT: O  778 MET cc_start: 0.8015 (mmt) cc_final: 0.7716 (mmt)
REVERT: O  858 GLN cc_start: 0.7696 (tp40) cc_final: 0.7444 (mt0)
REVERT: O 1026 MET cc_start: 0.2330 (mtp) cc_final: 0.1865 (ttp)
REVERT: O 1124 ARG cc_start: 0.7404 (mmm160) cc_final: 0.6989 (ptp-110)
REVERT: O 1182 ASP cc_start: 0.7151 (p0) cc_final: 0.6825 (p0)
REVERT: O 1185 TRP cc_start: 0.7461 (m100) cc_final: 0.6904 (m100)
REVERT: O 1218 GLU cc_start: 0.7118 (tt0) cc_final: 0.6820 (mt-10)
REVERT: O 1266 LYS cc_start: 0.6665 (mttt) cc_final: 0.6094 (tptp)
REVERT: O 1267 LYS cc_start: 0.7324 (mttt) cc_final: 0.6642 (tptt)
  outliers start: 25
  outliers final: 15
  residues processed: 214
  average time/residue: 0.1762
  time to fit residues: 52.8951
Evaluate side-chains
  180 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 165
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain H residue   39 ILE
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  111 VAL
Chi-restraints excluded: chain O residue  893 ILE
Chi-restraints excluded: chain O residue  907 SER
Chi-restraints excluded: chain O residue  949 VAL
Chi-restraints excluded: chain O residue 1013 CYS
Chi-restraints excluded: chain O residue 1188 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 120 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0770
   chunk 44 optimal weight:    0.7980
   chunk 157 optimal weight:    9.9990
   chunk 103 optimal weight:    9.9990
   chunk 25 optimal weight:    0.7980
   chunk 138 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 154 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.7338

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

Flipped N/Q/H residues before XYZ refinement:
D  84 ASN
G 110 ASN
O 776 GLN
** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O 928 GLN
** O 929 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O1019 GLN
O1186 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.142901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.104818 restraints weight = 36777.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.105837 restraints weight = 30089.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.106231 restraints weight = 24894.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.106395 restraints weight = 21959.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.106428 restraints weight = 20294.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  17964  Z= 0.152
  Angle     :  0.633  11.870  25490  Z= 0.357
  Chirality :  0.038   0.204   2892
  Planarity :  0.004   0.053   2204
  Dihedral  : 29.889 178.061   4733
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.79 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.23), residues: 1335
  helix:  0.93 (0.18), residues: 804
  sheet: -2.95 (0.54), residues: 63
  loop : -2.35 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  95 
 TYR   0.012   0.001   TYR D  83 
 PHE   0.027   0.002   PHE O1241 
 TRP   0.023   0.002   TRP O1083 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 (17964)
  covalent geometry    : angle       0.63349 (25490)
  hydrogen bonds       : bond        0.04336 (  851)
  hydrogen bonds       : angle       4.13750 ( 2268)

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

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

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 213
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.7276 (mm-30) cc_final: 0.7036 (mm-30)
REVERT: C   15 LYS cc_start: 0.8535 (mmtp) cc_final: 0.8226 (mtmm)
REVERT: D   59 MET cc_start: 0.8409 (tpp) cc_final: 0.8113 (tpp)
REVERT: D   95 GLN cc_start: 0.8257 (tt0) cc_final: 0.8034 (tt0)
REVERT: D  108 LYS cc_start: 0.8288 (tmtt) cc_final: 0.7972 (ttpt)
REVERT: E   41 TYR cc_start: 0.7932 (m-80) cc_final: 0.7641 (m-80)
REVERT: E  133 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7556 (mt-10)
REVERT: F   27 GLN cc_start: 0.8714 (mm110) cc_final: 0.8336 (mm-40)
REVERT: F   80 THR cc_start: 0.9211 (m) cc_final: 0.8933 (p)
REVERT: G   71 ARG cc_start: 0.7761 (mtp-110) cc_final: 0.7433 (ptp-170)
REVERT: O  990 PHE cc_start: 0.7203 (m-80) cc_final: 0.6829 (m-80)
REVERT: O 1026 MET cc_start: 0.2159 (mtp) cc_final: 0.1906 (ttp)
REVERT: O 1124 ARG cc_start: 0.7417 (mmm160) cc_final: 0.6855 (ptp-110)
REVERT: O 1182 ASP cc_start: 0.7295 (p0) cc_final: 0.6916 (p0)
REVERT: O 1218 GLU cc_start: 0.7283 (tt0) cc_final: 0.7032 (mt-10)
REVERT: O 1267 LYS cc_start: 0.7057 (mttt) cc_final: 0.6596 (tptt)
REVERT: O 1294 MET cc_start: 0.6459 (mmm) cc_final: 0.6166 (mmp)
  outliers start: 19
  outliers final: 5
  residues processed: 225
  average time/residue: 0.1610
  time to fit residues: 52.2687
Evaluate side-chains
  167 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 162
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue  893 ILE
Chi-restraints excluded: chain O residue  949 VAL
Chi-restraints excluded: chain O residue 1013 CYS
Chi-restraints excluded: chain O residue 1058 ILE
Chi-restraints excluded: chain O residue 1188 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 154 optimal weight:   10.0000
   chunk 9 optimal weight:    4.9990
   chunk 79 optimal weight:   10.0000
   chunk 68 optimal weight:    0.7980
   chunk 78 optimal weight:    8.9990
   chunk 66 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 127 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 50 optimal weight:    0.7980
   chunk 148 optimal weight:    0.0670
   overall best weight:    1.7322

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

Flipped N/Q/H residues before XYZ refinement:
H  95 GLN
O 783 ASN
** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.141069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.103957 restraints weight = 36824.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.102961 restraints weight = 37119.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.103784 restraints weight = 33136.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.104514 restraints weight = 25293.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.104564 restraints weight = 23251.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  17964  Z= 0.176
  Angle     :  0.644  13.173  25490  Z= 0.357
  Chirality :  0.038   0.170   2892
  Planarity :  0.004   0.052   2204
  Dihedral  : 29.799 174.248   4733
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.52 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 12.83 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.23), residues: 1335
  helix:  1.31 (0.19), residues: 806
  sheet: -2.72 (0.57), residues: 63
  loop : -2.13 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  72 
 TYR   0.014   0.002   TYR O1346 
 PHE   0.027   0.002   PHE O 946 
 TRP   0.048   0.003   TRP O1083 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (17964)
  covalent geometry    : angle       0.64407 (25490)
  hydrogen bonds       : bond        0.04683 (  851)
  hydrogen bonds       : angle       4.15767 ( 2268)

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

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

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.8422 (p) cc_final: 0.8163 (t)
REVERT: A   94 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7301 (mm-30)
REVERT: C   15 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8277 (mtmm)
REVERT: D   59 MET cc_start: 0.8525 (tpp) cc_final: 0.8220 (tpp)
REVERT: G   71 ARG cc_start: 0.7753 (mtp-110) cc_final: 0.7522 (ptp-170)
REVERT: H   95 GLN cc_start: 0.8347 (tt0) cc_final: 0.8108 (tt0)
REVERT: O  990 PHE cc_start: 0.7380 (m-80) cc_final: 0.7157 (m-80)
REVERT: O 1026 MET cc_start: 0.2200 (mtp) cc_final: 0.1899 (ttp)
REVERT: O 1119 MET cc_start: 0.8038 (mmm) cc_final: 0.7740 (mmm)
REVERT: O 1123 LEU cc_start: 0.7799 (mt) cc_final: 0.7503 (mp)
REVERT: O 1182 ASP cc_start: 0.7181 (p0) cc_final: 0.6884 (p0)
REVERT: O 1218 GLU cc_start: 0.7192 (tt0) cc_final: 0.6928 (mt-10)
REVERT: O 1294 MET cc_start: 0.6398 (mmm) cc_final: 0.6101 (mmp)
  outliers start: 22
  outliers final: 14
  residues processed: 184
  average time/residue: 0.1630
  time to fit residues: 42.9168
Evaluate side-chains
  174 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 160
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain O residue  754 ASP
Chi-restraints excluded: chain O residue  893 ILE
Chi-restraints excluded: chain O residue  907 SER
Chi-restraints excluded: chain O residue  949 VAL
Chi-restraints excluded: chain O residue 1013 CYS
Chi-restraints excluded: chain O residue 1027 LEU
Chi-restraints excluded: chain O residue 1058 ILE
Chi-restraints excluded: chain O residue 1188 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 102 optimal weight:   30.0000
   chunk 43 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 113 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 98 optimal weight:   10.0000
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.141227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.103683 restraints weight = 36870.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.102985 restraints weight = 37395.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.103466 restraints weight = 35893.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.104673 restraints weight = 27322.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.104558 restraints weight = 23863.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  17964  Z= 0.174
  Angle     :  0.635  14.304  25490  Z= 0.354
  Chirality :  0.038   0.171   2892
  Planarity :  0.004   0.054   2204
  Dihedral  : 29.647 172.408   4733
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.92 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 12.66 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.23), residues: 1335
  helix:  1.40 (0.19), residues: 821
  sheet: -2.56 (0.58), residues: 63
  loop : -1.83 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H  33 
 TYR   0.017   0.002   TYR C  57 
 PHE   0.024   0.002   PHE O 946 
 TRP   0.063   0.003   TRP O1083 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (17964)
  covalent geometry    : angle       0.63544 (25490)
  hydrogen bonds       : bond        0.04579 (  851)
  hydrogen bonds       : angle       4.09486 ( 2268)

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

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

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 170
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.8426 (p) cc_final: 0.8175 (t)
REVERT: A   94 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7410 (mm-30)
REVERT: C   15 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8278 (mtmm)
REVERT: D   59 MET cc_start: 0.8517 (tpp) cc_final: 0.8212 (tpp)
REVERT: D   76 GLU cc_start: 0.7826 (tp30) cc_final: 0.7313 (tp30)
REVERT: H   95 GLN cc_start: 0.8277 (tt0) cc_final: 0.8046 (tt0)
REVERT: O  834 GLU cc_start: 0.7332 (mm-30) cc_final: 0.6505 (mm-30)
REVERT: O 1022 MET cc_start: 0.3296 (tmm) cc_final: 0.3027 (tmm)
REVERT: O 1147 ARG cc_start: 0.7878 (tmm-80) cc_final: 0.7541 (tmm-80)
REVERT: O 1182 ASP cc_start: 0.7167 (p0) cc_final: 0.6927 (p0)
REVERT: O 1218 GLU cc_start: 0.7178 (tt0) cc_final: 0.6895 (mt-10)
REVERT: O 1294 MET cc_start: 0.6365 (mmm) cc_final: 0.6070 (mmp)
  outliers start: 23
  outliers final: 18
  residues processed: 185
  average time/residue: 0.1647
  time to fit residues: 43.4947
Evaluate side-chains
  176 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.511 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain O residue  754 ASP
Chi-restraints excluded: chain O residue  775 LEU
Chi-restraints excluded: chain O residue  893 ILE
Chi-restraints excluded: chain O residue  907 SER
Chi-restraints excluded: chain O residue  933 GLU
Chi-restraints excluded: chain O residue 1013 CYS
Chi-restraints excluded: chain O residue 1027 LEU
Chi-restraints excluded: chain O residue 1058 ILE
Chi-restraints excluded: chain O residue 1082 ILE
Chi-restraints excluded: chain O residue 1188 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 109 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 60 optimal weight:    7.9990
   chunk 125 optimal weight:    9.9990
   chunk 145 optimal weight:    7.9990
   chunk 88 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O1019 GLN
** O1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.141189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.103938 restraints weight = 36621.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.102945 restraints weight = 39308.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.103929 restraints weight = 35964.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.104196 restraints weight = 26075.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.104356 restraints weight = 24004.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.3823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  17964  Z= 0.181
  Angle     :  0.643  14.765  25490  Z= 0.355
  Chirality :  0.038   0.170   2892
  Planarity :  0.004   0.057   2204
  Dihedral  : 29.606 171.024   4733
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.51 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.24), residues: 1335
  helix:  1.50 (0.19), residues: 815
  sheet: -2.40 (0.60), residues: 63
  loop : -1.84 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG H  33 
 TYR   0.018   0.002   TYR D  83 
 PHE   0.025   0.002   PHE O 946 
 TRP   0.041   0.002   TRP O1083 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (17964)
  covalent geometry    : angle       0.64279 (25490)
  hydrogen bonds       : bond        0.04664 (  851)
  hydrogen bonds       : angle       4.09693 ( 2268)

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

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

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 167
  time to evaluate  : 0.581 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.8559 (p) cc_final: 0.8233 (t)
REVERT: A   94 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7418 (mm-30)
REVERT: C   15 LYS cc_start: 0.8548 (mmtp) cc_final: 0.8264 (mtmm)
REVERT: D   35 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6549 (pp20)
REVERT: D   59 MET cc_start: 0.8537 (tpp) cc_final: 0.8231 (tpp)
REVERT: D   76 GLU cc_start: 0.7969 (tp30) cc_final: 0.7531 (tp30)
REVERT: H   95 GLN cc_start: 0.8322 (tt0) cc_final: 0.8053 (tt0)
REVERT: O  782 PHE cc_start: 0.7275 (t80) cc_final: 0.6988 (t80)
REVERT: O  834 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6527 (mm-30)
REVERT: O 1182 ASP cc_start: 0.7279 (p0) cc_final: 0.7038 (p0)
REVERT: O 1294 MET cc_start: 0.6411 (mmm) cc_final: 0.6121 (mmp)
  outliers start: 25
  outliers final: 17
  residues processed: 182
  average time/residue: 0.1655
  time to fit residues: 43.0777
Evaluate side-chains
  174 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  111 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain O residue  754 ASP
Chi-restraints excluded: chain O residue  893 ILE
Chi-restraints excluded: chain O residue  907 SER
Chi-restraints excluded: chain O residue  933 GLU
Chi-restraints excluded: chain O residue 1013 CYS
Chi-restraints excluded: chain O residue 1027 LEU
Chi-restraints excluded: chain O residue 1188 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 91 optimal weight:    7.9990
   chunk 75 optimal weight:   10.0000
   chunk 155 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 104 optimal weight:    5.9990
   chunk 143 optimal weight:    6.9990
   chunk 142 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 93 optimal weight:    7.9990
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
C 104 GLN
** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1073 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.140943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.103517 restraints weight = 36807.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.102548 restraints weight = 37637.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.103061 restraints weight = 35218.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.104198 restraints weight = 27120.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.104120 restraints weight = 23706.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  17964  Z= 0.189
  Angle     :  0.652  14.609  25490  Z= 0.359
  Chirality :  0.038   0.168   2892
  Planarity :  0.004   0.059   2204
  Dihedral  : 29.570 170.031   4733
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.85 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.24), residues: 1335
  helix:  1.47 (0.19), residues: 819
  sheet: -2.33 (0.60), residues: 63
  loop : -1.71 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG H  33 
 TYR   0.018   0.002   TYR D  83 
 PHE   0.025   0.002   PHE O1063 
 TRP   0.036   0.002   TRP O1083 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (17964)
  covalent geometry    : angle       0.65152 (25490)
  hydrogen bonds       : bond        0.04730 (  851)
  hydrogen bonds       : angle       4.10381 ( 2268)

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

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

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 163
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.8575 (p) cc_final: 0.8281 (t)
REVERT: A   94 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7449 (mm-30)
REVERT: C   15 LYS cc_start: 0.8540 (mmtp) cc_final: 0.8257 (mtmm)
REVERT: C  111 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8482 (mt)
REVERT: D   35 GLU cc_start: 0.6840 (tm-30) cc_final: 0.6598 (pp20)
REVERT: D   59 MET cc_start: 0.8520 (tpp) cc_final: 0.8195 (tpp)
REVERT: D   76 GLU cc_start: 0.7882 (tp30) cc_final: 0.7471 (tp30)
REVERT: H   95 GLN cc_start: 0.8335 (tt0) cc_final: 0.8066 (tt0)
REVERT: O  782 PHE cc_start: 0.7063 (t80) cc_final: 0.6823 (t80)
REVERT: O  834 GLU cc_start: 0.7342 (mm-30) cc_final: 0.6531 (mm-30)
REVERT: O 1022 MET cc_start: 0.2966 (tmm) cc_final: 0.2540 (tmm)
REVERT: O 1182 ASP cc_start: 0.7212 (p0) cc_final: 0.6994 (p0)
REVERT: O 1294 MET cc_start: 0.6577 (mmm) cc_final: 0.6322 (mmp)
  outliers start: 27
  outliers final: 20
  residues processed: 178
  average time/residue: 0.1592
  time to fit residues: 40.9574
Evaluate side-chains
  175 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  111 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain O residue  754 ASP
Chi-restraints excluded: chain O residue  893 ILE
Chi-restraints excluded: chain O residue  907 SER
Chi-restraints excluded: chain O residue  908 LEU
Chi-restraints excluded: chain O residue  933 GLU
Chi-restraints excluded: chain O residue 1013 CYS
Chi-restraints excluded: chain O residue 1027 LEU
Chi-restraints excluded: chain O residue 1188 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 151 optimal weight:    0.0970
   chunk 33 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 141 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   chunk 134 optimal weight:    4.9990
   chunk 95 optimal weight:    7.9990
   chunk 92 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  49 HIS
** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O1073 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.144262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.107005 restraints weight = 37171.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.107082 restraints weight = 34695.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.107433 restraints weight = 33975.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.108270 restraints weight = 26141.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.108267 restraints weight = 23155.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  17964  Z= 0.143
  Angle     :  0.611  14.416  25490  Z= 0.338
  Chirality :  0.036   0.150   2892
  Planarity :  0.004   0.068   2204
  Dihedral  : 29.233 173.244   4733
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 14.95 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.24), residues: 1335
  helix:  1.71 (0.19), residues: 820
  sheet: -1.96 (0.63), residues: 63
  loop : -1.56 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG H  33 
 TYR   0.018   0.002   TYR C  57 
 PHE   0.028   0.002   PHE O 946 
 TRP   0.064   0.004   TRP O1083 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (17964)
  covalent geometry    : angle       0.61092 (25490)
  hydrogen bonds       : bond        0.03862 (  851)
  hydrogen bonds       : angle       3.85440 ( 2268)

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

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

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   59 MET cc_start: 0.8440 (tpp) cc_final: 0.8156 (tpp)
REVERT: D   76 GLU cc_start: 0.7799 (tp30) cc_final: 0.7452 (tp30)
REVERT: D   95 GLN cc_start: 0.8325 (tt0) cc_final: 0.8118 (tt0)
REVERT: D  108 LYS cc_start: 0.8219 (tmtt) cc_final: 0.7972 (ttpt)
REVERT: E  133 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7473 (mt-10)
REVERT: F   88 TYR cc_start: 0.8498 (m-80) cc_final: 0.8155 (m-10)
REVERT: H   46 LYS cc_start: 0.8786 (tppt) cc_final: 0.8428 (mmtp)
REVERT: H   95 GLN cc_start: 0.8197 (tt0) cc_final: 0.7964 (tt0)
REVERT: O  834 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6811 (mm-30)
REVERT: O  975 GLU cc_start: 0.4579 (tm-30) cc_final: 0.4352 (tm-30)
REVERT: O 1182 ASP cc_start: 0.6990 (p0) cc_final: 0.6761 (p0)
REVERT: O 1294 MET cc_start: 0.6459 (mmm) cc_final: 0.6105 (mmp)
  outliers start: 20
  outliers final: 16
  residues processed: 187
  average time/residue: 0.1560
  time to fit residues: 42.1840
Evaluate side-chains
  170 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  116 LEU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain O residue  754 ASP
Chi-restraints excluded: chain O residue  763 VAL
Chi-restraints excluded: chain O residue  893 ILE
Chi-restraints excluded: chain O residue  908 LEU
Chi-restraints excluded: chain O residue  933 GLU
Chi-restraints excluded: chain O residue 1013 CYS
Chi-restraints excluded: chain O residue 1027 LEU
Chi-restraints excluded: chain O residue 1188 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 144 optimal weight:    9.9990
   chunk 112 optimal weight:    7.9990
   chunk 55 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 111 optimal weight:    6.9990
   chunk 97 optimal weight:   10.0000
   chunk 156 optimal weight:    5.9990
   chunk 137 optimal weight:    3.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.140155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.102738 restraints weight = 37153.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.101896 restraints weight = 42316.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.102972 restraints weight = 39020.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.103342 restraints weight = 27615.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.103549 restraints weight = 26189.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.4290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  17964  Z= 0.231
  Angle     :  0.688  14.719  25490  Z= 0.376
  Chirality :  0.039   0.173   2892
  Planarity :  0.005   0.062   2204
  Dihedral  : 29.548 168.878   4733
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 15.46 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.24), residues: 1335
  helix:  1.33 (0.19), residues: 827
  sheet: -2.00 (0.63), residues: 63
  loop : -1.63 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H  33 
 TYR   0.021   0.002   TYR D  83 
 PHE   0.028   0.002   PHE O1063 
 TRP   0.101   0.004   TRP O1083 
 HIS   0.008   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 (17964)
  covalent geometry    : angle       0.68835 (25490)
  hydrogen bonds       : bond        0.05170 (  851)
  hydrogen bonds       : angle       4.23100 ( 2268)

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

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

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.8615 (p) cc_final: 0.8377 (t)
REVERT: D   59 MET cc_start: 0.8462 (tpp) cc_final: 0.8132 (tpp)
REVERT: D   76 GLU cc_start: 0.7849 (tp30) cc_final: 0.7485 (tp30)
REVERT: H   95 GLN cc_start: 0.8415 (tt0) cc_final: 0.8154 (tt0)
REVERT: O  834 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6558 (mm-30)
REVERT: O 1022 MET cc_start: 0.3135 (tmm) cc_final: 0.2646 (tmm)
REVERT: O 1182 ASP cc_start: 0.7107 (p0) cc_final: 0.6877 (p0)
REVERT: O 1294 MET cc_start: 0.6525 (mmm) cc_final: 0.6176 (mmp)
  outliers start: 20
  outliers final: 20
  residues processed: 167
  average time/residue: 0.1547
  time to fit residues: 37.9774
Evaluate side-chains
  169 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain G residue   85 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue  111 VAL
Chi-restraints excluded: chain O residue  754 ASP
Chi-restraints excluded: chain O residue  763 VAL
Chi-restraints excluded: chain O residue  893 ILE
Chi-restraints excluded: chain O residue  908 LEU
Chi-restraints excluded: chain O residue  933 GLU
Chi-restraints excluded: chain O residue 1013 CYS
Chi-restraints excluded: chain O residue 1027 LEU
Chi-restraints excluded: chain O residue 1188 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 76 optimal weight:    7.9990
   chunk 105 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 136 optimal weight:    0.8980
   chunk 148 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.144081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.105990 restraints weight = 36914.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.105807 restraints weight = 38198.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.106621 restraints weight = 30389.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.106837 restraints weight = 24472.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.106954 restraints weight = 23373.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.4584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  17964  Z= 0.151
  Angle     :  0.635  14.585  25490  Z= 0.348
  Chirality :  0.036   0.167   2892
  Planarity :  0.004   0.070   2204
  Dihedral  : 29.215 173.452   4733
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.14 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.59 (0.24), residues: 1335
  helix:  1.63 (0.19), residues: 820
  sheet: -1.83 (0.63), residues: 63
  loop : -1.63 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG H  33 
 TYR   0.018   0.001   TYR C  57 
 PHE   0.029   0.002   PHE O1122 
 TRP   0.115   0.004   TRP O1083 
 HIS   0.005   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (17964)
  covalent geometry    : angle       0.63512 (25490)
  hydrogen bonds       : bond        0.04010 (  851)
  hydrogen bonds       : angle       3.90896 ( 2268)

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

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

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2670 Ramachandran restraints generated.
    1335 Oldfield, 0 Emsley, 1335 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.7661 (pm20) cc_final: 0.7362 (pm20)
REVERT: A   87 SER cc_start: 0.8237 (p) cc_final: 0.7952 (t)
REVERT: D   59 MET cc_start: 0.8474 (tpp) cc_final: 0.8199 (tpp)
REVERT: D   95 GLN cc_start: 0.8311 (tt0) cc_final: 0.8085 (tt0)
REVERT: E  133 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7456 (mt-10)
REVERT: F   84 MET cc_start: 0.8047 (tpt) cc_final: 0.7549 (tmm)
REVERT: H   95 GLN cc_start: 0.8162 (tt0) cc_final: 0.7920 (tt0)
REVERT: O  834 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6797 (mm-30)
REVERT: O  975 GLU cc_start: 0.5117 (tm-30) cc_final: 0.4834 (tm-30)
REVERT: O 1022 MET cc_start: 0.2953 (tmm) cc_final: 0.2578 (tmm)
REVERT: O 1023 TYR cc_start: 0.4028 (t80) cc_final: 0.3422 (t80)
REVERT: O 1157 LEU cc_start: 0.5737 (mt) cc_final: 0.5130 (pt)
REVERT: O 1182 ASP cc_start: 0.7026 (p0) cc_final: 0.6745 (p0)
REVERT: O 1294 MET cc_start: 0.6520 (mmm) cc_final: 0.6160 (mmp)
  outliers start: 16
  outliers final: 14
  residues processed: 166
  average time/residue: 0.1498
  time to fit residues: 37.3095
Evaluate side-chains
  164 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 150
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain G residue   85 LEU
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain O residue  754 ASP
Chi-restraints excluded: chain O residue  763 VAL
Chi-restraints excluded: chain O residue  815 ILE
Chi-restraints excluded: chain O residue  893 ILE
Chi-restraints excluded: chain O residue  933 GLU
Chi-restraints excluded: chain O residue 1082 ILE
Chi-restraints excluded: chain O residue 1188 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 115 optimal weight:   10.0000
   chunk 156 optimal weight:   20.0000
   chunk 151 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 58 optimal weight:    0.9980
   chunk 128 optimal weight:    8.9990
   chunk 157 optimal weight:    6.9990
   chunk 141 optimal weight:    0.9990
   chunk 76 optimal weight:    8.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
** O 785 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.142095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.104330 restraints weight = 36993.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.104006 restraints weight = 34757.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.104716 restraints weight = 36256.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.105073 restraints weight = 26348.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.105220 restraints weight = 24037.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.4591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086  17964  Z= 0.184
  Angle     :  0.653  14.514  25490  Z= 0.357
  Chirality :  0.038   0.202   2892
  Planarity :  0.004   0.067   2204
  Dihedral  : 29.314 171.098   4733
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 16.48 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.24), residues: 1335
  helix:  1.58 (0.19), residues: 814
  sheet: -1.87 (0.63), residues: 63
  loop : -1.65 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG H  33 
 TYR   0.019   0.002   TYR C  57 
 PHE   0.025   0.002   PHE O1063 
 TRP   0.108   0.004   TRP O1083 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 (17964)
  covalent geometry    : angle       0.65288 (25490)
  hydrogen bonds       : bond        0.04510 (  851)
  hydrogen bonds       : angle       4.03501 ( 2268)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2502.92 seconds
wall clock time: 44 minutes 6.58 seconds (2646.58 seconds total)