Starting phenix.real_space_refine
on Thu Mar  5 07:46:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rja_4901/03_2026/6rja_4901.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rja_4901/03_2026/6rja_4901.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rja_4901/03_2026/6rja_4901.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rja_4901/03_2026/6rja_4901.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rja_4901/03_2026/6rja_4901.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rja_4901/03_2026/6rja_4901.cif"
  }
  resolution = 3.0
  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=   0.000 sd=   0.011
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     194      5.49       5
     S      50      5.16       5
     C   12214      2.51       5
     N    3522      2.21       5
     O    4392      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 98 residue(s): 0.02s

  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: 20372
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1506
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1506
          Classifications: {'peptide': 183}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 178}
    Chain: "C"
      Number of atoms: 6638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 815, 6638
          Classifications: {'peptide': 815}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 795}
          Chain breaks: 7
    Chain: "D"
      Number of atoms: 1656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 1656
          Classifications: {'RNA': 78}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 37, 'rna3p_pyr': 32}
          Link IDs: {'rna2p': 9, 'rna3p': 68}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 386
          Classifications: {'DNA': 19}
          Link IDs: {'rna3p': 18}
  Restraints were copied for chains:
    B, F, G, H
  Time building chain proxies: 7.72, per 1000 atoms: 0.38
  Number of scatterers: 20372
  At special positions: 0
  Unit cell: (120.015, 207.137, 107.569, 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      50     16.00
     P     194     15.00
     O    4392      8.00
     N    3522      7.00
     C   12214      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: 1.76
  Conformation dependent library (CDL) restraints added in 757.3 milliseconds
  

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3736

  Finding SS restraints...
    Secondary structure from input PDB file:
      74 helices and 20 sheets defined
      45.6% alpha, 13.8% beta
      64 base pairs and 115 stacking pairs defined.
    Time for finding SS restraints: 2.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 19
    Processing helix  chain 'A' and resid 21 through 25
    Processing helix  chain 'A' and resid 34 through 43
    Processing helix  chain 'A' and resid 47 through 51
      removed outlier: 3.774A  pdb=" N   LYS A  50 " --> pdb=" O   ASP A  47 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   MET A  51 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 47 through 51'
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 3.541A  pdb=" N   VAL A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 80
      removed outlier: 3.782A  pdb=" N   ALA A  70 " --> pdb=" O   ASP A  66 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   TYR A  80 " --> pdb=" O   GLN A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 89
    Processing helix  chain 'A' and resid 90 through 110
      removed outlier: 3.544A  pdb=" N   TYR A  94 " --> pdb=" O   PRO A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 178
    Processing helix  chain 'B' and resid 4 through 19
    Processing helix  chain 'B' and resid 21 through 25
    Processing helix  chain 'B' and resid 34 through 43
    Processing helix  chain 'B' and resid 47 through 51
      removed outlier: 3.775A  pdb=" N   LYS B  50 " --> pdb=" O   ASP B  47 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   MET B  51 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 47 through 51'
    Processing helix  chain 'B' and resid 52 through 64
      removed outlier: 3.540A  pdb=" N   VAL B  56 " --> pdb=" O   GLY B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 80
      removed outlier: 3.781A  pdb=" N   ALA B  70 " --> pdb=" O   ASP B  66 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   TYR B  80 " --> pdb=" O   GLN B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 89
    Processing helix  chain 'B' and resid 90 through 110
      removed outlier: 3.545A  pdb=" N   TYR B  94 " --> pdb=" O   PRO B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 178
    Processing helix  chain 'C' and resid 40 through 73
      removed outlier: 3.543A  pdb=" N   LEU C  44 " --> pdb=" O   ALA C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 95
    Processing helix  chain 'C' and resid 103 through 115
      removed outlier: 3.634A  pdb=" N   HIS C 115 " --> pdb=" O   ASN C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 134 through 147
    Processing helix  chain 'C' and resid 150 through 163
    Processing helix  chain 'C' and resid 185 through 204
      removed outlier: 3.813A  pdb=" N   TYR C 189 " --> pdb=" O   PRO C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 221
    Processing helix  chain 'C' and resid 250 through 254
      removed outlier: 4.007A  pdb=" N   ILE C 254 " --> pdb=" O   ILE C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 272 through 285
      removed outlier: 3.623A  pdb=" N   GLN C 276 " --> pdb=" O   SER C 272 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 311
    Processing helix  chain 'C' and resid 315 through 327
      removed outlier: 3.940A  pdb=" N   LEU C 327 " --> pdb=" O   ILE C 323 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 350 through 356
    Processing helix  chain 'C' and resid 369 through 382
    Processing helix  chain 'C' and resid 384 through 395
    Processing helix  chain 'C' and resid 402 through 416
      removed outlier: 3.812A  pdb=" N   VAL C 406 " --> pdb=" O   SER C 402 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 428 through 436
    Processing helix  chain 'C' and resid 445 through 454
    Processing helix  chain 'C' and resid 470 through 476
    Processing helix  chain 'C' and resid 479 through 500
    Processing helix  chain 'C' and resid 692 through 705
    Processing helix  chain 'C' and resid 737 through 748
    Processing helix  chain 'C' and resid 854 through 868
      removed outlier: 3.798A  pdb=" N   TYR C 858 " --> pdb=" O   THR C 854 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASP C 859 " --> pdb=" O   GLN C 855 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 869 through 871
      No H-bonds generated for 'chain 'C' and resid 869 through 871'
    Processing helix  chain 'C' and resid 872 through 878
      removed outlier: 3.772A  pdb=" N   ARG C 876 " --> pdb=" O   PHE C 872 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 878 through 891
      Proline residue:  C 888  - end of helix
      removed outlier: 3.717A  pdb=" N   GLU C 891 " --> pdb=" O   GLU C 887 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 910 through 918
    Processing helix  chain 'C' and resid 986 through 988
      No H-bonds generated for 'chain 'C' and resid 986 through 988'
    Processing helix  chain 'C' and resid 1000 through 1011
      removed outlier: 3.502A  pdb=" N   TYR C1004 " --> pdb=" O   SER C1000 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 40 through 73
      removed outlier: 3.544A  pdb=" N   LEU F  44 " --> pdb=" O   ALA F  40 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 87 through 95
    Processing helix  chain 'F' and resid 103 through 115
      removed outlier: 3.634A  pdb=" N   HIS F 115 " --> pdb=" O   ASN F 111 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 134 through 147
    Processing helix  chain 'F' and resid 150 through 163
    Processing helix  chain 'F' and resid 185 through 204
      removed outlier: 3.814A  pdb=" N   TYR F 189 " --> pdb=" O   PRO F 185 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 208 through 221
    Processing helix  chain 'F' and resid 250 through 254
      removed outlier: 4.006A  pdb=" N   ILE F 254 " --> pdb=" O   ILE F 251 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 272 through 285
      removed outlier: 3.624A  pdb=" N   GLN F 276 " --> pdb=" O   SER F 272 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 298 through 311
    Processing helix  chain 'F' and resid 315 through 327
      removed outlier: 3.940A  pdb=" N   LEU F 327 " --> pdb=" O   ILE F 323 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 350 through 356
    Processing helix  chain 'F' and resid 369 through 382
    Processing helix  chain 'F' and resid 384 through 395
    Processing helix  chain 'F' and resid 402 through 416
      removed outlier: 3.812A  pdb=" N   VAL F 406 " --> pdb=" O   SER F 402 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 428 through 436
    Processing helix  chain 'F' and resid 445 through 454
    Processing helix  chain 'F' and resid 470 through 476
    Processing helix  chain 'F' and resid 479 through 500
    Processing helix  chain 'F' and resid 692 through 705
    Processing helix  chain 'F' and resid 737 through 748
    Processing helix  chain 'F' and resid 854 through 868
      removed outlier: 3.798A  pdb=" N   TYR F 858 " --> pdb=" O   THR F 854 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ASP F 859 " --> pdb=" O   GLN F 855 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 869 through 871
      No H-bonds generated for 'chain 'F' and resid 869 through 871'
    Processing helix  chain 'F' and resid 872 through 878
      removed outlier: 3.771A  pdb=" N   ARG F 876 " --> pdb=" O   PHE F 872 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 878 through 891
      Proline residue:  F 888  - end of helix
      removed outlier: 3.717A  pdb=" N   GLU F 891 " --> pdb=" O   GLU F 887 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 910 through 918
    Processing helix  chain 'F' and resid 986 through 988
      No H-bonds generated for 'chain 'F' and resid 986 through 988'
    Processing helix  chain 'F' and resid 1000 through 1011
      removed outlier: 3.503A  pdb=" N   TYR F1004 " --> pdb=" O   SER F1000 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 122
      removed outlier: 6.634A  pdb=" N   ILE A 115 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   VAL A 136 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   GLY A 117 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   LEU A 134 " --> pdb=" O   GLY A 117 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   GLY A 119 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   MET A 121 " --> pdb=" O   ALA A 130 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   ALA A 130 " --> pdb=" O   MET A 121 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 144
      removed outlier: 6.648A  pdb=" N   SER A 147 " --> pdb=" O   LEU A 143 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 114 through 122
      removed outlier: 6.634A  pdb=" N   ILE B 115 " --> pdb=" O   VAL B 136 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   VAL B 136 " --> pdb=" O   ILE B 115 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   GLY B 117 " --> pdb=" O   LEU B 134 " (cutoff:3.500A)
      removed outlier: 4.680A  pdb=" N   LEU B 134 " --> pdb=" O   GLY B 117 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   GLY B 119 " --> pdb=" O   ALA B 132 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   MET B 121 " --> pdb=" O   ALA B 130 " (cutoff:3.500A)
      removed outlier: 5.457A  pdb=" N   ALA B 130 " --> pdb=" O   MET B 121 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 144
      removed outlier: 6.648A  pdb=" N   SER B 147 " --> pdb=" O   LEU B 143 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 710 through 712
      removed outlier: 3.764A  pdb=" N   ILE C  10 " --> pdb=" O   GLU C 509 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 168 through 172
    Processing sheet with id=AA7, first strand: chain 'C' and resid 268 through 269
      removed outlier: 3.746A  pdb=" N   ALA C 268 " --> pdb=" O   HIS C 425 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 935 through 941
      removed outlier: 3.509A  pdb=" N   LEU C 935 " --> pdb=" O   ILE C 849 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   VAL C 845 " --> pdb=" O   ASP C 939 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   LYS C 941 " --> pdb=" O   THR C 843 " (cutoff:3.500A)
      removed outlier: 8.281A  pdb=" N   THR C 843 " --> pdb=" O   LYS C 941 " (cutoff:3.500A)
      removed outlier: 5.398A  pdb=" N   ALA C 829 " --> pdb=" O   LEU C 846 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL C 958 " --> pdb=" O   TYR C 828 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 977 through 980
      removed outlier: 3.833A  pdb=" N   LYS C 977 " --> pdb=" O   ASN C 972 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASN C 972 " --> pdb=" O   LYS C 977 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   LEU C 983 " --> pdb=" O   TRP C 965 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 977 through 980
      removed outlier: 3.833A  pdb=" N   LYS C 977 " --> pdb=" O   ASN C 972 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASN C 972 " --> pdb=" O   LYS C 977 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ALA C 967 " --> pdb=" O   THR C1022 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   THR C1022 " --> pdb=" O   ALA C 967 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   VAL C 969 " --> pdb=" O   LYS C1020 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 989 through 990
    Processing sheet with id=AB3, first strand: chain 'C' and resid 1085 through 1088
      removed outlier: 4.273A  pdb=" N   CYS C1085 " --> pdb=" O   LEU C1058 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   GLU C1057 " --> pdb=" O   LEU C1045 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   LEU C1028 " --> pdb=" O   VAL C1099 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LYS C1098 " --> pdb=" O   ILE C1110 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 710 through 712
      removed outlier: 3.765A  pdb=" N   ILE F  10 " --> pdb=" O   GLU F 509 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 168 through 172
    Processing sheet with id=AB6, first strand: chain 'F' and resid 268 through 269
      removed outlier: 3.746A  pdb=" N   ALA F 268 " --> pdb=" O   HIS F 425 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 935 through 941
      removed outlier: 3.509A  pdb=" N   LEU F 935 " --> pdb=" O   ILE F 849 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   VAL F 845 " --> pdb=" O   ASP F 939 " (cutoff:3.500A)
      removed outlier: 5.052A  pdb=" N   LYS F 941 " --> pdb=" O   THR F 843 " (cutoff:3.500A)
      removed outlier: 8.281A  pdb=" N   THR F 843 " --> pdb=" O   LYS F 941 " (cutoff:3.500A)
      removed outlier: 5.398A  pdb=" N   ALA F 829 " --> pdb=" O   LEU F 846 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL F 958 " --> pdb=" O   TYR F 828 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'F' and resid 977 through 980
      removed outlier: 3.833A  pdb=" N   LYS F 977 " --> pdb=" O   ASN F 972 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ASN F 972 " --> pdb=" O   LYS F 977 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   LEU F 983 " --> pdb=" O   TRP F 965 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 977 through 980
      removed outlier: 3.833A  pdb=" N   LYS F 977 " --> pdb=" O   ASN F 972 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ASN F 972 " --> pdb=" O   LYS F 977 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   ALA F 967 " --> pdb=" O   THR F1022 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   THR F1022 " --> pdb=" O   ALA F 967 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   VAL F 969 " --> pdb=" O   LYS F1020 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 989 through 990
    Processing sheet with id=AC2, first strand: chain 'F' and resid 1085 through 1088
      removed outlier: 4.273A  pdb=" N   CYS F1085 " --> pdb=" O   LEU F1058 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   GLU F1057 " --> pdb=" O   LEU F1045 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   LEU F1028 " --> pdb=" O   VAL F1099 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LYS F1098 " --> pdb=" O   ILE F1110 " (cutoff:3.500A)

    726 hydrogen bonds defined for protein.
    2118 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      150 hydrogen bonds
      292 hydrogen bond angles
      0 basepair planarities
      64 basepair parallelities
      115 stacking parallelities
  Total time for adding SS restraints: 4.69

  Time building geometry restraints manager: 2.36 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: 4442
        1.33 -     1.45: 5508
        1.45 -     1.57: 10714
        1.57 -     1.69: 380
        1.69 -     1.81: 92
  Bond restraints: 21136
  Sorted by residual:
  bond pdb=" N   ILE C 436 "
       pdb=" CA  ILE C 436 "
    ideal  model  delta    sigma   weight residual
    1.464  1.485 -0.021 1.23e-02 6.61e+03 2.89e+00
  bond pdb=" N   ILE F 436 "
       pdb=" CA  ILE F 436 "
    ideal  model  delta    sigma   weight residual
    1.464  1.485 -0.021 1.23e-02 6.61e+03 2.87e+00
  bond pdb=" C   GLU C 887 "
       pdb=" N   PRO C 888 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.021 1.36e-02 5.41e+03 2.28e+00
  bond pdb=" C   GLU F 887 "
       pdb=" N   PRO F 888 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.020 1.36e-02 5.41e+03 2.20e+00
  bond pdb=" CA  GLU F 887 "
       pdb=" C   GLU F 887 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.018 1.26e-02 6.30e+03 2.14e+00
  ... (remaining 21131 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 28002
        1.90 -     3.80: 1143
        3.80 -     5.70: 134
        5.70 -     7.60: 15
        7.60 -     9.50: 8
  Bond angle restraints: 29302
  Sorted by residual:
  angle pdb=" C   ASN C  21 "
        pdb=" N   LYS C  22 "
        pdb=" CA  LYS C  22 "
      ideal   model   delta    sigma   weight residual
     121.54  131.04   -9.50 1.91e+00 2.74e-01 2.47e+01
  angle pdb=" C   ASN F  21 "
        pdb=" N   LYS F  22 "
        pdb=" CA  LYS F  22 "
      ideal   model   delta    sigma   weight residual
     121.54  130.99   -9.45 1.91e+00 2.74e-01 2.45e+01
  angle pdb=" CA  THR A 123 "
        pdb=" CB  THR A 123 "
        pdb=" CG2 THR A 123 "
      ideal   model   delta    sigma   weight residual
     110.50  116.77   -6.27 1.70e+00 3.46e-01 1.36e+01
  angle pdb=" CA  TYR B  26 "
        pdb=" CB  TYR B  26 "
        pdb=" CG  TYR B  26 "
      ideal   model   delta    sigma   weight residual
     113.90  120.53   -6.63 1.80e+00 3.09e-01 1.36e+01
  angle pdb=" CA  THR B 123 "
        pdb=" CB  THR B 123 "
        pdb=" CG2 THR B 123 "
      ideal   model   delta    sigma   weight residual
     110.50  116.76   -6.26 1.70e+00 3.46e-01 1.36e+01
  ... (remaining 29297 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 10987
       17.76 -    35.51: 1358
       35.51 -    53.27: 337
       53.27 -    71.03: 178
       71.03 -    88.78: 40
  Dihedral angle restraints: 12900
    sinusoidal: 7074
      harmonic: 5826
  Sorted by residual:
  dihedral pdb=" CA  GLN C1052 "
           pdb=" C   GLN C1052 "
           pdb=" N   LYS C1053 "
           pdb=" CA  LYS C1053 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.30  -26.70     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  GLN F1052 "
           pdb=" C   GLN F1052 "
           pdb=" N   LYS F1053 "
           pdb=" CA  LYS F1053 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.31  -26.69     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  GLU C 384 "
           pdb=" C   GLU C 384 "
           pdb=" N   ARG C 385 "
           pdb=" CA  ARG C 385 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.90  -24.10     0      5.00e+00 4.00e-02 2.32e+01
  ... (remaining 12897 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 2397
       0.050 -    0.100: 743
       0.100 -    0.149: 151
       0.149 -    0.199: 22
       0.199 -    0.249: 5
  Chirality restraints: 3318
  Sorted by residual:
  chirality pdb=" C1'   U D   7 "
            pdb=" O4'   U D   7 "
            pdb=" C2'   U D   7 "
            pdb=" N1    U D   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.22    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" C1'   U G   7 "
            pdb=" O4'   U G   7 "
            pdb=" C2'   U G   7 "
            pdb=" N1    U G   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.22    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" C1'   A G  68 "
            pdb=" O4'   A G  68 "
            pdb=" C2'   A G  68 "
            pdb=" N9    A G  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.25    0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 3315 not shown)

  Planarity restraints: 3048
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U G   7 "    0.033 2.00e-02 2.50e+03   1.84e-02 7.62e+00
        pdb=" N1    U G   7 "   -0.043 2.00e-02 2.50e+03
        pdb=" C2    U G   7 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    U G   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    U G   7 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    U G   7 "    0.002 2.00e-02 2.50e+03
        pdb=" O4    U G   7 "    0.010 2.00e-02 2.50e+03
        pdb=" C5    U G   7 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    U G   7 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U D   7 "   -0.032 2.00e-02 2.50e+03   1.83e-02 7.54e+00
        pdb=" N1    U D   7 "    0.043 2.00e-02 2.50e+03
        pdb=" C2    U D   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2    U D   7 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    U D   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    U D   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" O4    U D   7 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5    U D   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U D   7 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C 150 "   -0.040 5.00e-02 4.00e+02   6.09e-02 5.93e+00
        pdb=" N   PRO C 151 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO C 151 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO C 151 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 3045 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 6071
        2.83 -     3.35: 15898
        3.35 -     3.87: 33821
        3.87 -     4.38: 40115
        4.38 -     4.90: 64548
  Nonbonded interactions: 160453
  Sorted by model distance:
  nonbonded pdb=" O   SER F 101 "
            pdb=" OG  SER F 101 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   SER C 101 "
            pdb=" OG  SER C 101 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OH  TYR F 225 "
            pdb=" OG1 THR F 383 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" OH  TYR C 225 "
            pdb=" OG1 THR C 383 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   ALA F 376 "
            pdb=" OG1 THR F 380 "
     model   vdw
     2.351 3.040
  ... (remaining 160448 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'E'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     25.600
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:9.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  21136  Z= 0.254
  Angle     :  0.857   9.496  29302  Z= 0.471
  Chirality :  0.050   0.249   3318
  Planarity :  0.006   0.061   3048
  Dihedral  : 17.282  88.785   9164
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  8.09 %
    Favored  : 91.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.51 (0.15), residues: 1960
  helix: -1.92 (0.14), residues: 814
  sheet: -0.73 (0.33), residues: 234
  loop : -3.18 (0.15), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 223 
 TYR   0.029   0.002   TYR A  26 
 PHE   0.020   0.003   PHE F1042 
 TRP   0.010   0.002   TRP F 424 
 HIS   0.014   0.002   HIS C 877 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 (21136)
  covalent geometry    : angle       0.85717 (29302)
  hydrogen bonds       : bond        0.13800 (  872)
  hydrogen bonds       : angle       6.37483 ( 2410)

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 289
  time to evaluate  : 0.602 
Fit side-chains
REVERT: A  105 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8123 (ttpp)
REVERT: B   40 LYS cc_start: 0.8055 (mttt) cc_final: 0.7850 (mttm)
REVERT: B  105 LYS cc_start: 0.8375 (ttmm) cc_final: 0.7975 (tttp)
REVERT: C  314 MET cc_start: 0.5047 (tpt) cc_final: 0.4280 (mtp)
REVERT: C  355 LYS cc_start: 0.7583 (tptt) cc_final: 0.7027 (tptp)
REVERT: C  412 PHE cc_start: 0.7510 (t80) cc_final: 0.7294 (t80)
REVERT: C  844 TYR cc_start: 0.7876 (m-80) cc_final: 0.7545 (m-80)
REVERT: C 1010 LYS cc_start: 0.8312 (tptt) cc_final: 0.7939 (ttmt)
REVERT: C 1038 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6361 (mt-10)
REVERT: F  314 MET cc_start: 0.4953 (tpt) cc_final: 0.4296 (mtp)
REVERT: F  355 LYS cc_start: 0.7728 (tptt) cc_final: 0.7176 (tptp)
REVERT: F  844 TYR cc_start: 0.7915 (m-80) cc_final: 0.7657 (m-80)
REVERT: F 1010 LYS cc_start: 0.8220 (tptt) cc_final: 0.7811 (ttmt)
REVERT: F 1038 GLU cc_start: 0.6592 (mt-10) cc_final: 0.6344 (mt-10)
REVERT: F 1111 LYS cc_start: 0.7624 (tppt) cc_final: 0.6928 (tttt)
  outliers start: 4
  outliers final: 1
  residues processed: 291
  average time/residue: 0.5960
  time to fit residues: 195.3425
Evaluate side-chains
  197 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue  282 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 194 optimal weight:    0.5980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9990
   chunk 200 optimal weight:    1.9990
   chunk 212 optimal weight:    7.9990
   chunk 77 optimal weight:    5.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  37 ASN
A  78 ASN
A 101 GLN
A 127 ASN
A 151 GLN
A 177 ASN
B  37 ASN
B  78 ASN
B 101 GLN
B 127 ASN
B 151 GLN
B 177 ASN
C  31 ASN
C 231 ASN
C 279 ASN
C 282 ASN
C 285 ASN
C 303 GLN
C 405 GLN
C 416 ASN
C 494 ASN
C1039 GLN
C1081 ASN
C1112 ASN
F  31 ASN
F 231 ASN
F 279 ASN
F 282 ASN
F 285 ASN
F 302 ASN
F 303 GLN
F 348 HIS
F 405 GLN
F 416 ASN
** F 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F1039 GLN
F1081 ASN
F1112 ASN

Total number of N/Q/H flips: 37

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.201039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.162504 restraints weight = 24127.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 2.78
r_work: 0.3366 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  21136  Z= 0.119
  Angle     :  0.519   6.770  29302  Z= 0.282
  Chirality :  0.037   0.138   3318
  Planarity :  0.004   0.039   3048
  Dihedral  : 16.565  74.469   4984
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 14.31 %
    Favored  : 83.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.79 (0.17), residues: 1960
  helix:  0.13 (0.18), residues: 828
  sheet: -0.80 (0.31), residues: 258
  loop : -2.69 (0.16), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 385 
 TYR   0.026   0.001   TYR F 307 
 PHE   0.016   0.001   PHE F 412 
 TRP   0.008   0.001   TRP B  38 
 HIS   0.003   0.001   HIS C 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (21136)
  covalent geometry    : angle       0.51901 (29302)
  hydrogen bonds       : bond        0.04448 (  872)
  hydrogen bonds       : angle       4.48745 ( 2410)

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  267 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 223
  time to evaluate  : 0.701 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7830 (m-40) cc_final: 0.7588 (m-40)
REVERT: A  105 LYS cc_start: 0.8491 (ttmm) cc_final: 0.7969 (tttt)
REVERT: A  162 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7497 (pp20)
REVERT: B  105 LYS cc_start: 0.8492 (ttmm) cc_final: 0.7958 (tttm)
REVERT: B  145 SER cc_start: 0.8308 (t) cc_final: 0.8088 (m)
REVERT: B  162 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7608 (pp20)
REVERT: C  355 LYS cc_start: 0.6952 (tptt) cc_final: 0.6019 (tptp)
REVERT: C  385 ARG cc_start: 0.7934 (tmm-80) cc_final: 0.7656 (tmm-80)
REVERT: C  390 GLU cc_start: 0.8016 (tp30) cc_final: 0.7474 (tm-30)
REVERT: C  412 PHE cc_start: 0.6816 (t80) cc_final: 0.6521 (t80)
REVERT: C  432 MET cc_start: 0.6319 (tpp) cc_final: 0.5558 (ttp)
REVERT: C  844 TYR cc_start: 0.8223 (m-80) cc_final: 0.7925 (m-80)
REVERT: C  878 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.6046 (t70)
REVERT: C 1010 LYS cc_start: 0.8219 (tptt) cc_final: 0.7729 (ttmt)
REVERT: C 1038 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6106 (mt-10)
REVERT: F  355 LYS cc_start: 0.7138 (tptt) cc_final: 0.6264 (tptp)
REVERT: F  390 GLU cc_start: 0.7884 (tp30) cc_final: 0.7400 (tm-30)
REVERT: F  432 MET cc_start: 0.5950 (ttm) cc_final: 0.5611 (ttm)
REVERT: F  844 TYR cc_start: 0.8277 (m-80) cc_final: 0.7974 (m-80)
REVERT: F  878 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.5920 (t70)
REVERT: F 1010 LYS cc_start: 0.8227 (tptt) cc_final: 0.7676 (ttmt)
REVERT: F 1038 GLU cc_start: 0.6605 (mt-10) cc_final: 0.6074 (mt-10)
REVERT: F 1111 LYS cc_start: 0.7864 (tppt) cc_final: 0.6984 (tttt)
  outliers start: 44
  outliers final: 8
  residues processed: 248
  average time/residue: 0.6052
  time to fit residues: 169.7424
Evaluate side-chains
  200 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 188
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain C residue   14 SER
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain C residue  693 VAL
Chi-restraints excluded: chain C residue  878 ASP
Chi-restraints excluded: chain C residue 1066 PHE
Chi-restraints excluded: chain F residue   14 SER
Chi-restraints excluded: chain F residue  878 ASP
Chi-restraints excluded: chain F residue 1066 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 122 optimal weight:    6.9990
   chunk 213 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 142 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0770
   chunk 202 optimal weight:   10.0000
   chunk 209 optimal weight:    9.9990
   chunk 179 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 150 optimal weight:    0.3980
   overall best weight:    1.2942

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

Flipped N/Q/H residues before XYZ refinement:
B  78 ASN
** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 494 ASN
C1040 GLN
C1112 ASN
** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 348 HIS
** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 494 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.196822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.163700 restraints weight = 24051.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3818 rms_B_bonded: 2.29
r_work: 0.3287 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  21136  Z= 0.125
  Angle     :  0.502   7.333  29302  Z= 0.270
  Chirality :  0.036   0.138   3318
  Planarity :  0.003   0.035   3048
  Dihedral  : 16.388  74.357   4982
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.63 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.18), residues: 1960
  helix:  0.90 (0.18), residues: 828
  sheet: -0.57 (0.31), residues: 258
  loop : -2.44 (0.17), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 921 
 TYR   0.016   0.001   TYR B  26 
 PHE   0.015   0.001   PHE C1042 
 TRP   0.004   0.001   TRP A  38 
 HIS   0.003   0.001   HIS C 738 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (21136)
  covalent geometry    : angle       0.50190 (29302)
  hydrogen bonds       : bond        0.04397 (  872)
  hydrogen bonds       : angle       4.19879 ( 2410)

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 204
  time to evaluate  : 0.705 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7704 (m-40) cc_final: 0.7417 (m-40)
REVERT: A  105 LYS cc_start: 0.8449 (ttmm) cc_final: 0.7885 (tttm)
REVERT: A  162 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7489 (pp20)
REVERT: B  105 LYS cc_start: 0.8458 (ttmm) cc_final: 0.7906 (tttm)
REVERT: B  162 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7578 (pp20)
REVERT: C  349 THR cc_start: 0.4935 (OUTLIER) cc_final: 0.4700 (m)
REVERT: C  355 LYS cc_start: 0.6850 (tptt) cc_final: 0.5909 (tptp)
REVERT: C  390 GLU cc_start: 0.8048 (tp30) cc_final: 0.7413 (tm-30)
REVERT: C  412 PHE cc_start: 0.6664 (t80) cc_final: 0.6333 (t80)
REVERT: C  432 MET cc_start: 0.6351 (tpp) cc_final: 0.5762 (ttp)
REVERT: C  878 ASP cc_start: 0.6717 (OUTLIER) cc_final: 0.5726 (t70)
REVERT: C 1010 LYS cc_start: 0.8295 (tptt) cc_final: 0.7794 (ttmt)
REVERT: C 1038 GLU cc_start: 0.6582 (mt-10) cc_final: 0.5990 (mt-10)
REVERT: F  314 MET cc_start: 0.4864 (mmm) cc_final: 0.3848 (mtm)
REVERT: F  355 LYS cc_start: 0.7011 (tptt) cc_final: 0.6075 (tptp)
REVERT: F  390 GLU cc_start: 0.8007 (tp30) cc_final: 0.7413 (tm-30)
REVERT: F  432 MET cc_start: 0.5889 (OUTLIER) cc_final: 0.5646 (ttm)
REVERT: F  878 ASP cc_start: 0.6776 (OUTLIER) cc_final: 0.5726 (t70)
REVERT: F 1010 LYS cc_start: 0.8261 (tptt) cc_final: 0.7677 (ttmt)
REVERT: F 1038 GLU cc_start: 0.6516 (mt-10) cc_final: 0.5961 (mt-10)
REVERT: F 1111 LYS cc_start: 0.7896 (tppt) cc_final: 0.6994 (tttt)
  outliers start: 40
  outliers final: 14
  residues processed: 224
  average time/residue: 0.6064
  time to fit residues: 154.4748
Evaluate side-chains
  204 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 184
  time to evaluate  : 0.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  349 THR
Chi-restraints excluded: chain C residue  394 HIS
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  693 VAL
Chi-restraints excluded: chain C residue  878 ASP
Chi-restraints excluded: chain C residue  885 VAL
Chi-restraints excluded: chain C residue 1062 ASP
Chi-restraints excluded: chain C residue 1066 PHE
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  383 THR
Chi-restraints excluded: chain F residue  394 HIS
Chi-restraints excluded: chain F residue  432 MET
Chi-restraints excluded: chain F residue  878 ASP
Chi-restraints excluded: chain F residue  885 VAL
Chi-restraints excluded: chain F residue 1066 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 30 optimal weight:    0.4980
   chunk 149 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0060
   chunk 52 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 157 optimal weight:    7.9990
   chunk 188 optimal weight:    3.9990
   chunk 147 optimal weight:    0.8980
   overall best weight:    1.0798

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

Flipped N/Q/H residues before XYZ refinement:
A  78 ASN
A 109 ASN
** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 446 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1112 ASN
** F 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 348 HIS
** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 494 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.201934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.170074 restraints weight = 24285.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 2.40
r_work: 0.3345 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  21136  Z= 0.112
  Angle     :  0.481   9.868  29302  Z= 0.257
  Chirality :  0.035   0.136   3318
  Planarity :  0.003   0.034   3048
  Dihedral  : 16.269  74.316   4982
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 16.35 %
    Favored  : 80.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.18), residues: 1960
  helix:  1.33 (0.19), residues: 830
  sheet: -0.50 (0.31), residues: 258
  loop : -2.25 (0.17), residues: 872

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F 921 
 TYR   0.015   0.001   TYR A  26 
 PHE   0.015   0.001   PHE C1042 
 TRP   0.005   0.001   TRP A  38 
 HIS   0.003   0.001   HIS C 348 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (21136)
  covalent geometry    : angle       0.48093 (29302)
  hydrogen bonds       : bond        0.03937 (  872)
  hydrogen bonds       : angle       4.03471 ( 2410)

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 200
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 ASN cc_start: 0.7685 (m-40) cc_final: 0.7352 (m-40)
REVERT: A  105 LYS cc_start: 0.8488 (ttmm) cc_final: 0.7959 (tttm)
REVERT: A  145 SER cc_start: 0.8286 (t) cc_final: 0.8015 (m)
REVERT: A  162 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7628 (pp20)
REVERT: B   43 ASN cc_start: 0.7574 (m110) cc_final: 0.7070 (m-40)
REVERT: B   89 MET cc_start: 0.8484 (ptp) cc_final: 0.8251 (ptm)
REVERT: B  105 LYS cc_start: 0.8519 (ttmm) cc_final: 0.7981 (tttm)
REVERT: B  162 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7671 (pp20)
REVERT: C  355 LYS cc_start: 0.6947 (tptt) cc_final: 0.6001 (tptp)
REVERT: C  390 GLU cc_start: 0.8068 (tp30) cc_final: 0.7348 (tm-30)
REVERT: C  408 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7288 (pp20)
REVERT: C  412 PHE cc_start: 0.6772 (t80) cc_final: 0.6450 (t80)
REVERT: C  432 MET cc_start: 0.6309 (tpp) cc_final: 0.5812 (ttp)
REVERT: C  878 ASP cc_start: 0.6686 (OUTLIER) cc_final: 0.5710 (t70)
REVERT: C 1010 LYS cc_start: 0.8247 (tptt) cc_final: 0.7729 (ttmt)
REVERT: C 1038 GLU cc_start: 0.6665 (mt-10) cc_final: 0.6113 (mt-10)
REVERT: F  282 ASN cc_start: 0.5806 (m110) cc_final: 0.5463 (m110)
REVERT: F  355 LYS cc_start: 0.7118 (tptt) cc_final: 0.6168 (tptp)
REVERT: F  390 GLU cc_start: 0.8017 (tp30) cc_final: 0.7341 (tm-30)
REVERT: F  878 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.5691 (t70)
REVERT: F 1010 LYS cc_start: 0.8248 (tptt) cc_final: 0.7710 (ttmt)
REVERT: F 1038 GLU cc_start: 0.6641 (mt-10) cc_final: 0.6087 (mt-10)
REVERT: F 1073 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7685 (pt)
REVERT: F 1111 LYS cc_start: 0.7866 (tppt) cc_final: 0.7000 (tttt)
  outliers start: 54
  outliers final: 19
  residues processed: 229
  average time/residue: 0.6401
  time to fit residues: 165.8483
Evaluate side-chains
  209 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain B residue  110 ASN
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain C residue   14 SER
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  408 GLU
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  693 VAL
Chi-restraints excluded: chain C residue  838 ASP
Chi-restraints excluded: chain C residue  862 MET
Chi-restraints excluded: chain C residue  878 ASP
Chi-restraints excluded: chain C residue 1066 PHE
Chi-restraints excluded: chain F residue   14 SER
Chi-restraints excluded: chain F residue  394 HIS
Chi-restraints excluded: chain F residue  492 ILE
Chi-restraints excluded: chain F residue  693 VAL
Chi-restraints excluded: chain F residue  814 VAL
Chi-restraints excluded: chain F residue  878 ASP
Chi-restraints excluded: chain F residue 1027 ASP
Chi-restraints excluded: chain F residue 1062 ASP
Chi-restraints excluded: chain F residue 1073 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 193 optimal weight:    3.9990
   chunk 75 optimal weight:    0.2980
   chunk 163 optimal weight:    0.9990
   chunk 180 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 171 optimal weight:    1.9990
   chunk 198 optimal weight:   10.0000
   chunk 129 optimal weight:    3.9990
   chunk 161 optimal weight:    4.9990
   chunk 183 optimal weight:    6.9990
   chunk 37 optimal weight:   10.0000
   overall best weight:    2.2588

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

Flipped N/Q/H residues before XYZ refinement:
** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 813 GLN
C1112 ASN
F 178 HIS
F 348 HIS
** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.198469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.166641 restraints weight = 24079.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 2.31
r_work: 0.3316 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  21136  Z= 0.175
  Angle     :  0.553  12.965  29302  Z= 0.294
  Chirality :  0.038   0.150   3318
  Planarity :  0.004   0.032   3048
  Dihedral  : 16.298  74.350   4982
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 16.86 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.63 (0.18), residues: 1960
  helix:  1.23 (0.18), residues: 832
  sheet: -0.52 (0.32), residues: 254
  loop : -2.11 (0.18), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 921 
 TYR   0.018   0.002   TYR C 215 
 PHE   0.016   0.002   PHE C1042 
 TRP   0.004   0.002   TRP A 106 
 HIS   0.004   0.001   HIS F 425 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 (21136)
  covalent geometry    : angle       0.55282 (29302)
  hydrogen bonds       : bond        0.05052 (  872)
  hydrogen bonds       : angle       4.12062 ( 2410)

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 196
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASN cc_start: 0.7750 (m-40) cc_final: 0.7510 (m-40)
REVERT: A  105 LYS cc_start: 0.8597 (ttmm) cc_final: 0.8081 (tttt)
REVERT: A  113 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.8082 (t0)
REVERT: A  162 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7751 (pp20)
REVERT: B   43 ASN cc_start: 0.7740 (m110) cc_final: 0.7309 (m-40)
REVERT: B  105 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8117 (tttt)
REVERT: B  162 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7714 (pp20)
REVERT: C  355 LYS cc_start: 0.6933 (tptt) cc_final: 0.5968 (tptp)
REVERT: C  390 GLU cc_start: 0.8122 (tp30) cc_final: 0.7303 (tm-30)
REVERT: C  408 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7269 (pp20)
REVERT: C  412 PHE cc_start: 0.6780 (t80) cc_final: 0.6426 (t80)
REVERT: C  432 MET cc_start: 0.6296 (tpp) cc_final: 0.5824 (ttp)
REVERT: C  878 ASP cc_start: 0.6709 (OUTLIER) cc_final: 0.5698 (t70)
REVERT: C  916 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7205 (tt0)
REVERT: C 1010 LYS cc_start: 0.8253 (tptt) cc_final: 0.7813 (ttmt)
REVERT: C 1038 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6160 (mt-10)
REVERT: F  355 LYS cc_start: 0.7192 (tptt) cc_final: 0.6218 (tptp)
REVERT: F  390 GLU cc_start: 0.8083 (tp30) cc_final: 0.7313 (tm-30)
REVERT: F  408 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7403 (pp20)
REVERT: F  432 MET cc_start: 0.4947 (ttm) cc_final: 0.4709 (ptm)
REVERT: F  878 ASP cc_start: 0.6606 (OUTLIER) cc_final: 0.5582 (t70)
REVERT: F 1010 LYS cc_start: 0.8219 (tptt) cc_final: 0.7804 (ttmt)
REVERT: F 1038 GLU cc_start: 0.6737 (mt-10) cc_final: 0.6162 (mt-10)
REVERT: F 1111 LYS cc_start: 0.7901 (tppt) cc_final: 0.7021 (tttt)
  outliers start: 62
  outliers final: 28
  residues processed: 233
  average time/residue: 0.5678
  time to fit residues: 151.2217
Evaluate side-chains
  222 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 186
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain B residue  110 ASN
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain C residue   14 SER
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  383 THR
Chi-restraints excluded: chain C residue  394 HIS
Chi-restraints excluded: chain C residue  408 GLU
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  738 HIS
Chi-restraints excluded: chain C residue  814 VAL
Chi-restraints excluded: chain C residue  838 ASP
Chi-restraints excluded: chain C residue  878 ASP
Chi-restraints excluded: chain C residue  916 GLU
Chi-restraints excluded: chain C residue 1066 PHE
Chi-restraints excluded: chain F residue   14 SER
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  274 THR
Chi-restraints excluded: chain F residue  383 THR
Chi-restraints excluded: chain F residue  394 HIS
Chi-restraints excluded: chain F residue  408 GLU
Chi-restraints excluded: chain F residue  493 VAL
Chi-restraints excluded: chain F residue  693 VAL
Chi-restraints excluded: chain F residue  738 HIS
Chi-restraints excluded: chain F residue  814 VAL
Chi-restraints excluded: chain F residue  838 ASP
Chi-restraints excluded: chain F residue  878 ASP
Chi-restraints excluded: chain F residue 1027 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 131 optimal weight:    0.8980
   chunk 62 optimal weight:   10.0000
   chunk 0 optimal weight:    7.9990
   chunk 116 optimal weight:    5.9990
   chunk 163 optimal weight:    5.9990
   chunk 211 optimal weight:    5.9990
   chunk 156 optimal weight:    8.9990
   chunk 194 optimal weight:    1.9990
   overall best weight:    1.9384

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

Flipped N/Q/H residues before XYZ refinement:
C 178 HIS
** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C1112 ASN
F 178 HIS
F 348 HIS
** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.198836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.166751 restraints weight = 23906.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3867 rms_B_bonded: 2.28
r_work: 0.3318 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  21136  Z= 0.154
  Angle     :  0.526   7.362  29302  Z= 0.281
  Chirality :  0.037   0.145   3318
  Planarity :  0.003   0.033   3048
  Dihedral  : 16.181  74.394   4982
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 17.08 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.46 (0.18), residues: 1960
  helix:  1.38 (0.18), residues: 830
  sheet: -0.10 (0.33), residues: 234
  loop : -2.09 (0.17), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 921 
 TYR   0.018   0.001   TYR B  26 
 PHE   0.016   0.001   PHE C1042 
 TRP   0.005   0.001   TRP A  38 
 HIS   0.003   0.001   HIS C 738 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (21136)
  covalent geometry    : angle       0.52620 (29302)
  hydrogen bonds       : bond        0.04641 (  872)
  hydrogen bonds       : angle       4.05708 ( 2410)

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 193
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASN cc_start: 0.7765 (m-40) cc_final: 0.7516 (m-40)
REVERT: A  105 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8043 (tttm)
REVERT: A  162 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7800 (pp20)
REVERT: B   43 ASN cc_start: 0.7694 (m110) cc_final: 0.7243 (m-40)
REVERT: B  105 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8055 (tttm)
REVERT: B  162 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7776 (pp20)
REVERT: C  137 GLN cc_start: 0.8162 (mp10) cc_final: 0.7894 (mp10)
REVERT: C  355 LYS cc_start: 0.6987 (tptt) cc_final: 0.6039 (tptp)
REVERT: C  390 GLU cc_start: 0.8145 (tp30) cc_final: 0.7335 (tm-30)
REVERT: C  408 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7184 (pp20)
REVERT: C  412 PHE cc_start: 0.6770 (t80) cc_final: 0.6472 (t80)
REVERT: C  432 MET cc_start: 0.6220 (tpp) cc_final: 0.5817 (ttp)
REVERT: C  810 PHE cc_start: 0.6903 (m-80) cc_final: 0.6639 (m-10)
REVERT: C  878 ASP cc_start: 0.6752 (OUTLIER) cc_final: 0.5814 (t70)
REVERT: C 1010 LYS cc_start: 0.8276 (tptt) cc_final: 0.7838 (ttmt)
REVERT: C 1038 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6226 (mt-10)
REVERT: F  355 LYS cc_start: 0.7228 (tptt) cc_final: 0.6349 (tptp)
REVERT: F  390 GLU cc_start: 0.8128 (tp30) cc_final: 0.7331 (tm-30)
REVERT: F  408 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7459 (pp20)
REVERT: F  432 MET cc_start: 0.4894 (ttm) cc_final: 0.4624 (ptm)
REVERT: F  878 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.5689 (t70)
REVERT: F 1010 LYS cc_start: 0.8280 (tptt) cc_final: 0.7841 (ttmt)
REVERT: F 1038 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6250 (mt-10)
REVERT: F 1111 LYS cc_start: 0.7908 (tppt) cc_final: 0.7039 (tttt)
  outliers start: 70
  outliers final: 32
  residues processed: 237
  average time/residue: 0.5438
  time to fit residues: 147.6160
Evaluate side-chains
  227 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 189
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain B residue  110 ASN
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain C residue   14 SER
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  383 THR
Chi-restraints excluded: chain C residue  394 HIS
Chi-restraints excluded: chain C residue  408 GLU
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  693 VAL
Chi-restraints excluded: chain C residue  738 HIS
Chi-restraints excluded: chain C residue  814 VAL
Chi-restraints excluded: chain C residue  838 ASP
Chi-restraints excluded: chain C residue  878 ASP
Chi-restraints excluded: chain C residue 1027 ASP
Chi-restraints excluded: chain C residue 1112 ASN
Chi-restraints excluded: chain F residue   14 SER
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  383 THR
Chi-restraints excluded: chain F residue  394 HIS
Chi-restraints excluded: chain F residue  408 GLU
Chi-restraints excluded: chain F residue  493 VAL
Chi-restraints excluded: chain F residue  693 VAL
Chi-restraints excluded: chain F residue  738 HIS
Chi-restraints excluded: chain F residue  814 VAL
Chi-restraints excluded: chain F residue  838 ASP
Chi-restraints excluded: chain F residue  878 ASP
Chi-restraints excluded: chain F residue 1027 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 138 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 178 optimal weight:    4.9990
   chunk 198 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0010
   chunk 173 optimal weight:    5.9990
   chunk 163 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 197 optimal weight:    0.8980
   chunk 203 optimal weight:    0.6980
   overall best weight:    1.7190

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

Flipped N/Q/H residues before XYZ refinement:
A 127 ASN
B 127 ASN
** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C1112 ASN
F 348 HIS
** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.199493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.166988 restraints weight = 24144.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 2.29
r_work: 0.3325 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  21136  Z= 0.142
  Angle     :  0.514   7.475  29302  Z= 0.275
  Chirality :  0.037   0.151   3318
  Planarity :  0.003   0.035   3048
  Dihedral  : 16.162  74.421   4982
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.10 %
    Favored  : 78.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.18), residues: 1960
  helix:  1.49 (0.18), residues: 832
  sheet: -0.05 (0.33), residues: 234
  loop : -2.04 (0.18), residues: 894

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 921 
 TYR   0.018   0.001   TYR B  26 
 PHE   0.016   0.001   PHE C1042 
 TRP   0.005   0.001   TRP A  38 
 HIS   0.003   0.001   HIS F 738 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (21136)
  covalent geometry    : angle       0.51446 (29302)
  hydrogen bonds       : bond        0.04469 (  872)
  hydrogen bonds       : angle       4.00932 ( 2410)

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 191
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASN cc_start: 0.7730 (m-40) cc_final: 0.7445 (m-40)
REVERT: A  105 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8041 (tttm)
REVERT: A  162 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7785 (pp20)
REVERT: B   43 ASN cc_start: 0.7721 (m110) cc_final: 0.7254 (m-40)
REVERT: B  105 LYS cc_start: 0.8603 (ttmm) cc_final: 0.8061 (tttm)
REVERT: B  162 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7782 (pp20)
REVERT: C  137 GLN cc_start: 0.8171 (mp10) cc_final: 0.7950 (mp10)
REVERT: C  355 LYS cc_start: 0.7000 (tptt) cc_final: 0.6046 (tptp)
REVERT: C  390 GLU cc_start: 0.8123 (tp30) cc_final: 0.7301 (tm-30)
REVERT: C  408 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7299 (pp20)
REVERT: C  412 PHE cc_start: 0.6744 (t80) cc_final: 0.6440 (t80)
REVERT: C  432 MET cc_start: 0.6225 (tpp) cc_final: 0.5837 (ttp)
REVERT: C  810 PHE cc_start: 0.6773 (m-80) cc_final: 0.6538 (m-10)
REVERT: C  878 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.5788 (t70)
REVERT: C  919 TYR cc_start: 0.7661 (m-10) cc_final: 0.7182 (m-80)
REVERT: C 1010 LYS cc_start: 0.8278 (tptt) cc_final: 0.7832 (ttmt)
REVERT: C 1038 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6190 (mt-10)
REVERT: F  146 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6711 (tp)
REVERT: F  355 LYS cc_start: 0.7178 (tptt) cc_final: 0.6290 (tptp)
REVERT: F  370 GLU cc_start: 0.6335 (pp20) cc_final: 0.5965 (pm20)
REVERT: F  390 GLU cc_start: 0.8122 (tp30) cc_final: 0.7315 (tm-30)
REVERT: F  408 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7239 (pp20)
REVERT: F  810 PHE cc_start: 0.6707 (m-80) cc_final: 0.6442 (m-10)
REVERT: F  878 ASP cc_start: 0.6692 (OUTLIER) cc_final: 0.5696 (t70)
REVERT: F 1010 LYS cc_start: 0.8288 (tptt) cc_final: 0.7836 (ttmt)
REVERT: F 1038 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6204 (mt-10)
REVERT: F 1111 LYS cc_start: 0.7900 (tppt) cc_final: 0.7033 (tttt)
  outliers start: 60
  outliers final: 34
  residues processed: 229
  average time/residue: 0.5603
  time to fit residues: 146.6173
Evaluate side-chains
  222 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 181
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 MET
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain B residue  110 ASN
Chi-restraints excluded: chain B residue  118 THR
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain C residue   14 SER
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  383 THR
Chi-restraints excluded: chain C residue  394 HIS
Chi-restraints excluded: chain C residue  408 GLU
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  693 VAL
Chi-restraints excluded: chain C residue  738 HIS
Chi-restraints excluded: chain C residue  814 VAL
Chi-restraints excluded: chain C residue  838 ASP
Chi-restraints excluded: chain C residue  878 ASP
Chi-restraints excluded: chain C residue 1027 ASP
Chi-restraints excluded: chain C residue 1062 ASP
Chi-restraints excluded: chain F residue   14 SER
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  274 THR
Chi-restraints excluded: chain F residue  383 THR
Chi-restraints excluded: chain F residue  394 HIS
Chi-restraints excluded: chain F residue  408 GLU
Chi-restraints excluded: chain F residue  493 VAL
Chi-restraints excluded: chain F residue  693 VAL
Chi-restraints excluded: chain F residue  738 HIS
Chi-restraints excluded: chain F residue  814 VAL
Chi-restraints excluded: chain F residue  838 ASP
Chi-restraints excluded: chain F residue  862 MET
Chi-restraints excluded: chain F residue  878 ASP
Chi-restraints excluded: chain F residue 1027 ASP
Chi-restraints excluded: chain F residue 1062 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 208 optimal weight:    6.9990
   chunk 83 optimal weight:   20.0000
   chunk 92 optimal weight:    0.7980
   chunk 197 optimal weight:   10.0000
   chunk 95 optimal weight:    0.7980
   chunk 41 optimal weight:    0.8980
   chunk 210 optimal weight:    4.9990
   chunk 112 optimal weight:    0.0270
   chunk 88 optimal weight:    0.9980
   chunk 16 optimal weight:    0.4980
   chunk 212 optimal weight:    7.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 737 HIS
C 813 GLN
F 348 HIS
** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.203732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.165910 restraints weight = 24254.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 2.68
r_work: 0.3416 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  21136  Z= 0.093
  Angle     :  0.459   7.648  29302  Z= 0.245
  Chirality :  0.035   0.153   3318
  Planarity :  0.003   0.033   3048
  Dihedral  : 16.061  74.365   4982
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 19.17 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.19), residues: 1960
  helix:  1.84 (0.19), residues: 834
  sheet:  0.07 (0.32), residues: 238
  loop : -1.94 (0.18), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F 921 
 TYR   0.016   0.001   TYR F 162 
 PHE   0.014   0.001   PHE C1042 
 TRP   0.005   0.001   TRP A  38 
 HIS   0.003   0.001   HIS C 737 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 (21136)
  covalent geometry    : angle       0.45896 (29302)
  hydrogen bonds       : bond        0.03345 (  872)
  hydrogen bonds       : angle       3.83852 ( 2410)

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 199
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7624 (m-40) cc_final: 0.7320 (m-40)
REVERT: A  105 LYS cc_start: 0.8430 (ttmm) cc_final: 0.7919 (tttm)
REVERT: A  162 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7574 (pp20)
REVERT: B   43 ASN cc_start: 0.7501 (m110) cc_final: 0.7045 (m-40)
REVERT: B  105 LYS cc_start: 0.8445 (ttmm) cc_final: 0.7897 (tttm)
REVERT: B  162 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7569 (pp20)
REVERT: C  355 LYS cc_start: 0.6876 (tptt) cc_final: 0.5989 (tptp)
REVERT: C  370 GLU cc_start: 0.6228 (pp20) cc_final: 0.5876 (pm20)
REVERT: C  390 GLU cc_start: 0.7969 (tp30) cc_final: 0.7252 (tm-30)
REVERT: C  412 PHE cc_start: 0.6592 (t80) cc_final: 0.6308 (t80)
REVERT: C  878 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.5710 (t70)
REVERT: C 1010 LYS cc_start: 0.8239 (tptt) cc_final: 0.7717 (ttmt)
REVERT: C 1038 GLU cc_start: 0.6538 (mt-10) cc_final: 0.5918 (mt-10)
REVERT: F  314 MET cc_start: 0.5760 (tpp) cc_final: 0.3859 (ptt)
REVERT: F  355 LYS cc_start: 0.7044 (tptt) cc_final: 0.6091 (tptp)
REVERT: F  370 GLU cc_start: 0.6236 (pp20) cc_final: 0.5864 (pm20)
REVERT: F  385 ARG cc_start: 0.7802 (tmm-80) cc_final: 0.7184 (ptm-80)
REVERT: F  390 GLU cc_start: 0.7986 (tp30) cc_final: 0.7321 (tm-30)
REVERT: F  408 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7039 (pp20)
REVERT: F  432 MET cc_start: 0.4698 (OUTLIER) cc_final: 0.3938 (tpp)
REVERT: F  810 PHE cc_start: 0.6567 (m-80) cc_final: 0.6354 (m-10)
REVERT: F  878 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.5728 (t70)
REVERT: F 1010 LYS cc_start: 0.8230 (tptt) cc_final: 0.7704 (ttmt)
REVERT: F 1038 GLU cc_start: 0.6548 (mt-10) cc_final: 0.5990 (mt-10)
  outliers start: 48
  outliers final: 22
  residues processed: 227
  average time/residue: 0.5633
  time to fit residues: 145.8526
Evaluate side-chains
  207 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 179
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain C residue   14 SER
Chi-restraints excluded: chain C residue  350 PHE
Chi-restraints excluded: chain C residue  383 THR
Chi-restraints excluded: chain C residue  394 HIS
Chi-restraints excluded: chain C residue  447 MET
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain C residue  693 VAL
Chi-restraints excluded: chain C residue  738 HIS
Chi-restraints excluded: chain C residue  814 VAL
Chi-restraints excluded: chain C residue  878 ASP
Chi-restraints excluded: chain C residue 1027 ASP
Chi-restraints excluded: chain F residue   14 SER
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  383 THR
Chi-restraints excluded: chain F residue  408 GLU
Chi-restraints excluded: chain F residue  432 MET
Chi-restraints excluded: chain F residue  693 VAL
Chi-restraints excluded: chain F residue  738 HIS
Chi-restraints excluded: chain F residue  862 MET
Chi-restraints excluded: chain F residue  878 ASP
Chi-restraints excluded: chain F residue 1027 ASP
Chi-restraints excluded: chain F residue 1056 VAL
Chi-restraints excluded: chain F residue 1062 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 88 optimal weight:    0.6980
   chunk 135 optimal weight:    0.9980
   chunk 185 optimal weight:    6.9990
   chunk 212 optimal weight:    8.9990
   chunk 177 optimal weight:    0.7980
   chunk 138 optimal weight:    3.9990
   chunk 207 optimal weight:    6.9990
   chunk 165 optimal weight:    9.9990
   chunk 193 optimal weight:    5.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B 109 ASN
C  67 ASN
C 178 HIS
** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 737 HIS
C 813 GLN
F  67 ASN
F 178 HIS
F 348 HIS
** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.201052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.168378 restraints weight = 23953.378|
|-----------------------------------------------------------------------------|
r_work (start): 0.3888 rms_B_bonded: 2.35
r_work: 0.3343 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  21136  Z= 0.122
  Angle     :  0.494   8.566  29302  Z= 0.262
  Chirality :  0.036   0.142   3318
  Planarity :  0.003   0.035   3048
  Dihedral  : 16.055  74.369   4982
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.80 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.00 (0.19), residues: 1960
  helix:  1.81 (0.19), residues: 838
  sheet:  0.21 (0.33), residues: 226
  loop : -1.94 (0.18), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 921 
 TYR   0.016   0.001   TYR F 307 
 PHE   0.014   0.001   PHE C1042 
 TRP   0.003   0.001   TRP F 424 
 HIS   0.003   0.001   HIS F 738 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (21136)
  covalent geometry    : angle       0.49372 (29302)
  hydrogen bonds       : bond        0.03988 (  872)
  hydrogen bonds       : angle       3.85545 ( 2410)

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 180
  time to evaluate  : 0.703 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7670 (m-40) cc_final: 0.7341 (m-40)
REVERT: A  105 LYS cc_start: 0.8559 (ttmm) cc_final: 0.8012 (tttm)
REVERT: A  139 GLU cc_start: 0.8306 (tt0) cc_final: 0.8097 (tt0)
REVERT: A  162 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7724 (pp20)
REVERT: B   43 ASN cc_start: 0.7608 (m110) cc_final: 0.7144 (m-40)
REVERT: B   89 MET cc_start: 0.8354 (ptp) cc_final: 0.8137 (ptm)
REVERT: B  105 LYS cc_start: 0.8554 (ttmm) cc_final: 0.8015 (tttm)
REVERT: B  162 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7662 (pp20)
REVERT: C  355 LYS cc_start: 0.7050 (tptt) cc_final: 0.6145 (tptp)
REVERT: C  370 GLU cc_start: 0.6354 (pp20) cc_final: 0.5974 (pm20)
REVERT: C  390 GLU cc_start: 0.8079 (tp30) cc_final: 0.7304 (tm-30)
REVERT: C  412 PHE cc_start: 0.6729 (t80) cc_final: 0.6441 (t80)
REVERT: C  432 MET cc_start: 0.5218 (ttp) cc_final: 0.4979 (ptm)
REVERT: C  878 ASP cc_start: 0.6821 (OUTLIER) cc_final: 0.5800 (t70)
REVERT: C  919 TYR cc_start: 0.7674 (m-10) cc_final: 0.7196 (m-80)
REVERT: C 1010 LYS cc_start: 0.8245 (tptt) cc_final: 0.7849 (ttmt)
REVERT: C 1038 GLU cc_start: 0.6493 (mt-10) cc_final: 0.5912 (mt-10)
REVERT: F  146 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.6586 (tp)
REVERT: F  178 HIS cc_start: 0.7277 (OUTLIER) cc_final: 0.7007 (p-80)
REVERT: F  314 MET cc_start: 0.6010 (tpp) cc_final: 0.4093 (ptt)
REVERT: F  355 LYS cc_start: 0.7115 (tptt) cc_final: 0.6266 (tptp)
REVERT: F  370 GLU cc_start: 0.6352 (pp20) cc_final: 0.5929 (pm20)
REVERT: F  390 GLU cc_start: 0.8054 (tp30) cc_final: 0.7326 (tm-30)
REVERT: F  408 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7202 (pp20)
REVERT: F  878 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.5776 (t70)
REVERT: F 1010 LYS cc_start: 0.8263 (tptt) cc_final: 0.7857 (ttmt)
REVERT: F 1038 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6096 (mt-10)
  outliers start: 43
  outliers final: 28
  residues processed: 209
  average time/residue: 0.5962
  time to fit residues: 142.5230
Evaluate side-chains
  211 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 176
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ASN
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain C residue   14 SER
Chi-restraints excluded: chain C residue  383 THR
Chi-restraints excluded: chain C residue  394 HIS
Chi-restraints excluded: chain C residue  447 MET
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  693 VAL
Chi-restraints excluded: chain C residue  738 HIS
Chi-restraints excluded: chain C residue  814 VAL
Chi-restraints excluded: chain C residue  838 ASP
Chi-restraints excluded: chain C residue  862 MET
Chi-restraints excluded: chain C residue  878 ASP
Chi-restraints excluded: chain C residue 1027 ASP
Chi-restraints excluded: chain C residue 1056 VAL
Chi-restraints excluded: chain F residue   14 SER
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  178 HIS
Chi-restraints excluded: chain F residue  383 THR
Chi-restraints excluded: chain F residue  394 HIS
Chi-restraints excluded: chain F residue  408 GLU
Chi-restraints excluded: chain F residue  493 VAL
Chi-restraints excluded: chain F residue  693 VAL
Chi-restraints excluded: chain F residue  738 HIS
Chi-restraints excluded: chain F residue  838 ASP
Chi-restraints excluded: chain F residue  862 MET
Chi-restraints excluded: chain F residue  878 ASP
Chi-restraints excluded: chain F residue 1027 ASP
Chi-restraints excluded: chain F residue 1056 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 6 optimal weight:    0.4980
   chunk 186 optimal weight:    9.9990
   chunk 167 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 171 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0870
   chunk 28 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0970
   chunk 138 optimal weight:    4.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 737 HIS
C 813 GLN
F 348 HIS
** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.197695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.164839 restraints weight = 23855.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 2.29
r_work: 0.3314 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.113  21136  Z= 0.158
  Angle     :  0.914  61.599  29302  Z= 0.490
  Chirality :  0.036   0.196   3318
  Planarity :  0.004   0.147   3048
  Dihedral  : 16.071  74.426   4982
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 19.97 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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:  0.01 (0.19), residues: 1960
  helix:  1.82 (0.19), residues: 838
  sheet:  0.19 (0.33), residues: 226
  loop : -1.93 (0.18), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 921 
 TYR   0.015   0.001   TYR B  26 
 PHE   0.013   0.001   PHE C1042 
 TRP   0.003   0.001   TRP A  38 
 HIS   0.185   0.004   HIS F 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (21136)
  covalent geometry    : angle       0.91438 (29302)
  hydrogen bonds       : bond        0.03999 (  872)
  hydrogen bonds       : angle       3.86858 ( 2410)

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

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

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3920 Ramachandran restraints generated.
    1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 176
  time to evaluate  : 0.685 
Fit side-chains
REVERT: A   43 ASN cc_start: 0.7609 (m-40) cc_final: 0.7260 (m-40)
REVERT: A  105 LYS cc_start: 0.8465 (ttmm) cc_final: 0.7865 (tttm)
REVERT: A  139 GLU cc_start: 0.8208 (tt0) cc_final: 0.7999 (tt0)
REVERT: A  162 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7503 (pp20)
REVERT: B   43 ASN cc_start: 0.7512 (m110) cc_final: 0.7006 (m-40)
REVERT: B   89 MET cc_start: 0.8298 (ptp) cc_final: 0.8078 (ptm)
REVERT: B  105 LYS cc_start: 0.8451 (ttmm) cc_final: 0.7866 (tttm)
REVERT: B  162 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7488 (pp20)
REVERT: C  355 LYS cc_start: 0.6924 (tptt) cc_final: 0.6047 (tptp)
REVERT: C  370 GLU cc_start: 0.6247 (pp20) cc_final: 0.5889 (pm20)
REVERT: C  390 GLU cc_start: 0.7994 (tp30) cc_final: 0.7256 (tm-30)
REVERT: C  408 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6972 (pp20)
REVERT: C  412 PHE cc_start: 0.6599 (t80) cc_final: 0.6314 (t80)
REVERT: C  432 MET cc_start: 0.5130 (ttp) cc_final: 0.4901 (ptm)
REVERT: C  446 GLN cc_start: 0.3968 (OUTLIER) cc_final: 0.3088 (mt0)
REVERT: C  878 ASP cc_start: 0.6814 (OUTLIER) cc_final: 0.5748 (t70)
REVERT: C  919 TYR cc_start: 0.7648 (m-10) cc_final: 0.7161 (m-80)
REVERT: C 1010 LYS cc_start: 0.8206 (tptt) cc_final: 0.7743 (ttmt)
REVERT: F  146 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6553 (tp)
REVERT: F  314 MET cc_start: 0.5939 (tpp) cc_final: 0.3991 (ptt)
REVERT: F  355 LYS cc_start: 0.7034 (tptt) cc_final: 0.6197 (tptp)
REVERT: F  370 GLU cc_start: 0.6266 (pp20) cc_final: 0.5863 (pm20)
REVERT: F  385 ARG cc_start: 0.7751 (tmm-80) cc_final: 0.7177 (ptm-80)
REVERT: F  390 GLU cc_start: 0.7978 (tp30) cc_final: 0.7246 (tm-30)
REVERT: F  408 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7171 (pp20)
REVERT: F  810 PHE cc_start: 0.6643 (m-80) cc_final: 0.6372 (m-10)
REVERT: F  878 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.5731 (t70)
REVERT: F 1010 LYS cc_start: 0.8211 (tptt) cc_final: 0.7742 (ttmt)
REVERT: F 1038 GLU cc_start: 0.6537 (mt-10) cc_final: 0.5922 (mt-10)
  outliers start: 40
  outliers final: 27
  residues processed: 204
  average time/residue: 0.5686
  time to fit residues: 132.6163
Evaluate side-chains
  210 residues out of total 1768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 175
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 GLU
Chi-restraints excluded: chain A residue  166 SER
Chi-restraints excluded: chain B residue  162 GLU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain C residue   14 SER
Chi-restraints excluded: chain C residue  383 THR
Chi-restraints excluded: chain C residue  394 HIS
Chi-restraints excluded: chain C residue  408 GLU
Chi-restraints excluded: chain C residue  446 GLN
Chi-restraints excluded: chain C residue  447 MET
Chi-restraints excluded: chain C residue  481 VAL
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  693 VAL
Chi-restraints excluded: chain C residue  738 HIS
Chi-restraints excluded: chain C residue  814 VAL
Chi-restraints excluded: chain C residue  862 MET
Chi-restraints excluded: chain C residue  878 ASP
Chi-restraints excluded: chain C residue 1027 ASP
Chi-restraints excluded: chain C residue 1056 VAL
Chi-restraints excluded: chain F residue   14 SER
Chi-restraints excluded: chain F residue  113 VAL
Chi-restraints excluded: chain F residue  146 LEU
Chi-restraints excluded: chain F residue  178 HIS
Chi-restraints excluded: chain F residue  383 THR
Chi-restraints excluded: chain F residue  394 HIS
Chi-restraints excluded: chain F residue  408 GLU
Chi-restraints excluded: chain F residue  493 VAL
Chi-restraints excluded: chain F residue  693 VAL
Chi-restraints excluded: chain F residue  738 HIS
Chi-restraints excluded: chain F residue  814 VAL
Chi-restraints excluded: chain F residue  862 MET
Chi-restraints excluded: chain F residue  878 ASP
Chi-restraints excluded: chain F residue 1027 ASP
Chi-restraints excluded: chain F residue 1056 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 214
   random chunks:
   chunk 179 optimal weight:    0.3980
   chunk 42 optimal weight:    1.9990
   chunk 188 optimal weight:    0.7980
   chunk 92 optimal weight:    0.2980
   chunk 6 optimal weight:    0.4980
   chunk 157 optimal weight:    0.9990
   chunk 85 optimal weight:    7.9990
   chunk 183 optimal weight:    4.9990
   chunk 126 optimal weight:    8.9990
   chunk 193 optimal weight:    5.9990
   chunk 195 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C 178 HIS
** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 737 HIS
C 813 GLN
F 178 HIS
F 348 HIS
** F 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.202974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.165851 restraints weight = 24161.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 2.70
r_work: 0.3392 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  21136  Z= 0.096
  Angle     :  0.475  10.001  29302  Z= 0.251
  Chirality :  0.035   0.154   3318
  Planarity :  0.003   0.034   3048
  Dihedral  : 16.039  74.406   4982
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 20.19 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.12 (0.19), residues: 1960
  helix:  1.92 (0.19), residues: 838
  sheet:  0.23 (0.33), residues: 230
  loop : -1.88 (0.18), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F 385 
 TYR   0.014   0.001   TYR F 162 
 PHE   0.014   0.001   PHE C1042 
 TRP   0.005   0.001   TRP A  38 
 HIS   0.003   0.001   HIS C 737 

Details of bonding type rmsd
  covalent geometry    : bond        0.00203 (21136)
  covalent geometry    : angle       0.47472 (29302)
  hydrogen bonds       : bond        0.03521 (  872)
  hydrogen bonds       : angle       3.81039 ( 2410)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 5954.25 seconds
wall clock time: 102 minutes 20.53 seconds (6140.53 seconds total)