Starting phenix.real_space_refine
on Sat Aug 23 05:53:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fvd_50803/08_2025/9fvd_50803.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fvd_50803/08_2025/9fvd_50803.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fvd_50803/08_2025/9fvd_50803.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fvd_50803/08_2025/9fvd_50803.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fvd_50803/08_2025/9fvd_50803.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fvd_50803/08_2025/9fvd_50803.cif"
  }
  resolution = 3.2
  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=   0.001
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      54      5.49       5
     S      15      5.16       5
     C    6240      2.51       5
     N    1833      2.21       5
     O    2004      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10146
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2991
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 2991
          Classifications: {'peptide': 381}
          Link IDs: {'PTRANS': 10, 'TRANS': 370}
          Chain breaks: 2
    Chain: "S"
      Number of atoms: 391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 391
          Classifications: {'RNA': 18}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 11, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 3, 'rna3p': 14}
    Chain: "R"
      Number of atoms: 261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 261
          Classifications: {'RNA': 12}
          Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 2, 'rna3p': 9}
    Chain: "Q"
      Number of atoms: 130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 130
          Classifications: {'RNA': 6}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 1, 'rna3p': 4}
    Chain: "U"
      Number of atoms: 260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 260
          Classifications: {'RNA': 12}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 7, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 2, 'rna3p': 9}
    Chain: "T"
      Number of atoms: 131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 131
          Classifications: {'RNA': 6}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1}
          Link IDs: {'rna2p': 1, 'rna3p': 4}
  Restraints were copied for chains:
    B, C
  Residues with excluded nonbonded symmetry interactions: 54
    residue:
      pdb=" P     A S   1 " occ=0.33
      ... (21 atoms not shown)
      pdb=" OP3   A S   1 " occ=0.33
    residue:
      pdb=" P     G S   2 " occ=0.33
      ... (21 atoms not shown)
      pdb=" C4    G S   2 " occ=0.33
    residue:
      pdb=" P     A S   3 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S   3 " occ=0.33
    residue:
      pdb=" P     C S   4 " occ=0.33
      ... (18 atoms not shown)
      pdb=" C6    C S   4 " occ=0.33
    residue:
      pdb=" P     A S   5 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S   5 " occ=0.33
    residue:
      pdb=" P     C S   6 " occ=0.33
      ... (18 atoms not shown)
      pdb=" C6    C S   6 " occ=0.33
    residue:
      pdb=" P     A S   7 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S   7 " occ=0.33
    residue:
      pdb=" P     C S   8 " occ=0.33
      ... (18 atoms not shown)
      pdb=" C6    C S   8 " occ=0.33
    residue:
      pdb=" P     A S   9 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S   9 " occ=0.33
    residue:
      pdb=" P     A S  10 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S  10 " occ=0.33
    residue:
      pdb=" P     A S  11 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S  11 " occ=0.33
    residue:
      pdb=" P     A S  12 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S  12 " occ=0.33
    ... (remaining 42 not shown)
  Time building chain proxies: 2.18, per 1000 atoms: 0.21
  Number of scatterers: 10146
  At special positions: 0
  Unit cell: (86.49, 125.55, 102.3, 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      15     16.00
     P      54     15.00
     O    2004      8.00
     N    1833      7.00
     C    6240      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: 1.16
  Conformation dependent library (CDL) restraints added in 339.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2136

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 6 sheets defined
      76.9% alpha, 4.2% beta
      21 base pairs and 36 stacking pairs defined.
    Time for finding SS restraints: 1.83
  Creating SS restraints...
    Processing helix  chain 'B' and resid 4 through 13
      removed outlier: 4.442A  pdb=" N   LEU B  10 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   GLY B  11 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS B  13 " --> pdb=" O   LEU B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 45
    Processing helix  chain 'B' and resid 51 through 67
      removed outlier: 4.518A  pdb=" N   GLY B  55 " --> pdb=" O   ASP B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 75
    Processing helix  chain 'B' and resid 76 through 86
    Processing helix  chain 'B' and resid 99 through 104
      removed outlier: 4.292A  pdb=" N   VAL B 103 " --> pdb=" O   ARG B  99 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE B 104 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 99 through 104'
    Processing helix  chain 'B' and resid 110 through 118
    Processing helix  chain 'B' and resid 129 through 139
    Processing helix  chain 'B' and resid 148 through 165
    Processing helix  chain 'B' and resid 171 through 175
    Processing helix  chain 'B' and resid 176 through 190
    Processing helix  chain 'B' and resid 190 through 204
      removed outlier: 4.080A  pdb=" N   LYS B 194 " --> pdb=" O   SER B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 223
    Processing helix  chain 'B' and resid 227 through 237
    Processing helix  chain 'B' and resid 249 through 252
      removed outlier: 3.673A  pdb=" N   ARG B 252 " --> pdb=" O   PRO B 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 249 through 252'
    Processing helix  chain 'B' and resid 253 through 272
      removed outlier: 4.132A  pdb=" N   GLU B 259 " --> pdb=" O   LYS B 255 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ARG B 272 " --> pdb=" O   SER B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 278
      No H-bonds generated for 'chain 'B' and resid 276 through 278'
    Processing helix  chain 'B' and resid 279 through 284
    Processing helix  chain 'B' and resid 287 through 292
      removed outlier: 3.659A  pdb=" N   GLU B 292 " --> pdb=" O   ASN B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 311
    Processing helix  chain 'B' and resid 312 through 317
    Processing helix  chain 'B' and resid 323 through 350
      removed outlier: 3.782A  pdb=" N   ALA B 350 " --> pdb=" O   ILE B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 391
      removed outlier: 3.509A  pdb=" N   ARG B 356 " --> pdb=" O   ASP B 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4 through 13
      removed outlier: 4.442A  pdb=" N   LEU A  10 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   GLY A  11 " --> pdb=" O   LEU A   8 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS A  13 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 45
    Processing helix  chain 'A' and resid 51 through 67
      removed outlier: 4.519A  pdb=" N   GLY A  55 " --> pdb=" O   ASP A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 75
    Processing helix  chain 'A' and resid 76 through 86
    Processing helix  chain 'A' and resid 99 through 104
      removed outlier: 4.292A  pdb=" N   VAL A 103 " --> pdb=" O   ARG A  99 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE A 104 " --> pdb=" O   PHE A 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 99 through 104'
    Processing helix  chain 'A' and resid 110 through 118
    Processing helix  chain 'A' and resid 129 through 139
    Processing helix  chain 'A' and resid 148 through 165
    Processing helix  chain 'A' and resid 171 through 175
    Processing helix  chain 'A' and resid 176 through 190
    Processing helix  chain 'A' and resid 190 through 204
      removed outlier: 4.080A  pdb=" N   LYS A 194 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 223
    Processing helix  chain 'A' and resid 227 through 237
    Processing helix  chain 'A' and resid 249 through 252
      removed outlier: 3.673A  pdb=" N   ARG A 252 " --> pdb=" O   PRO A 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 249 through 252'
    Processing helix  chain 'A' and resid 253 through 272
      removed outlier: 4.132A  pdb=" N   GLU A 259 " --> pdb=" O   LYS A 255 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ARG A 272 " --> pdb=" O   SER A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 278
      No H-bonds generated for 'chain 'A' and resid 276 through 278'
    Processing helix  chain 'A' and resid 279 through 284
    Processing helix  chain 'A' and resid 287 through 292
      removed outlier: 3.659A  pdb=" N   GLU A 292 " --> pdb=" O   ASN A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 311
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 323 through 350
      removed outlier: 3.782A  pdb=" N   ALA A 350 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 391
      removed outlier: 3.509A  pdb=" N   ARG A 356 " --> pdb=" O   ASP A 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 13
      removed outlier: 4.441A  pdb=" N   LEU C  10 " --> pdb=" O   LEU C   7 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   GLY C  11 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS C  13 " --> pdb=" O   LEU C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 45
    Processing helix  chain 'C' and resid 51 through 67
      removed outlier: 4.518A  pdb=" N   GLY C  55 " --> pdb=" O   ASP C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 75
    Processing helix  chain 'C' and resid 76 through 86
    Processing helix  chain 'C' and resid 99 through 104
      removed outlier: 4.292A  pdb=" N   VAL C 103 " --> pdb=" O   ARG C  99 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE C 104 " --> pdb=" O   PHE C 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 99 through 104'
    Processing helix  chain 'C' and resid 110 through 118
    Processing helix  chain 'C' and resid 129 through 139
    Processing helix  chain 'C' and resid 148 through 165
    Processing helix  chain 'C' and resid 171 through 175
    Processing helix  chain 'C' and resid 176 through 190
    Processing helix  chain 'C' and resid 190 through 204
      removed outlier: 4.081A  pdb=" N   LYS C 194 " --> pdb=" O   SER C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 223
    Processing helix  chain 'C' and resid 227 through 237
    Processing helix  chain 'C' and resid 249 through 252
      removed outlier: 3.673A  pdb=" N   ARG C 252 " --> pdb=" O   PRO C 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 249 through 252'
    Processing helix  chain 'C' and resid 253 through 272
      removed outlier: 4.131A  pdb=" N   GLU C 259 " --> pdb=" O   LYS C 255 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ARG C 272 " --> pdb=" O   SER C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 276 through 278
      No H-bonds generated for 'chain 'C' and resid 276 through 278'
    Processing helix  chain 'C' and resid 279 through 284
    Processing helix  chain 'C' and resid 287 through 292
      removed outlier: 3.659A  pdb=" N   GLU C 292 " --> pdb=" O   ASN C 289 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 296 through 311
    Processing helix  chain 'C' and resid 312 through 317
    Processing helix  chain 'C' and resid 323 through 350
      removed outlier: 3.783A  pdb=" N   ALA C 350 " --> pdb=" O   ILE C 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 352 through 391
      removed outlier: 3.509A  pdb=" N   ARG C 356 " --> pdb=" O   ASP C 352 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 27
    Processing sheet with id=AA2, first strand: chain 'B' and resid 238 through 241
    Processing sheet with id=AA3, first strand: chain 'A' and resid 22 through 27
    Processing sheet with id=AA4, first strand: chain 'A' and resid 238 through 241
    Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 27
    Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 241

    609 hydrogen bonds defined for protein.
    1719 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      42 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      21 basepair parallelities
      36 stacking parallelities
  Total time for adding SS restraints: 1.65

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3229
        1.34 -     1.46: 2166
        1.46 -     1.57: 4931
        1.57 -     1.69: 103
        1.69 -     1.81: 21
  Bond restraints: 10450
  Sorted by residual:
  bond pdb=" CG1 ILE A 198 "
       pdb=" CD1 ILE A 198 "
    ideal  model  delta    sigma   weight residual
    1.513  1.474  0.039 3.90e-02 6.57e+02 9.97e-01
  bond pdb=" CG1 ILE C 198 "
       pdb=" CD1 ILE C 198 "
    ideal  model  delta    sigma   weight residual
    1.513  1.475  0.038 3.90e-02 6.57e+02 9.71e-01
  bond pdb=" CG1 ILE B 198 "
       pdb=" CD1 ILE B 198 "
    ideal  model  delta    sigma   weight residual
    1.513  1.475  0.038 3.90e-02 6.57e+02 9.57e-01
  bond pdb=" CA  ASP C 148 "
       pdb=" CB  ASP C 148 "
    ideal  model  delta    sigma   weight residual
    1.534  1.547 -0.013 1.45e-02 4.76e+03 7.76e-01
  bond pdb=" CA  ASP A 148 "
       pdb=" CB  ASP A 148 "
    ideal  model  delta    sigma   weight residual
    1.534  1.546 -0.012 1.45e-02 4.76e+03 7.27e-01
  ... (remaining 10445 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 13911
        1.52 -     3.03: 410
        3.03 -     4.55: 62
        4.55 -     6.07: 18
        6.07 -     7.59: 3
  Bond angle restraints: 14404
  Sorted by residual:
  angle pdb=" CA  ARG C  83 "
        pdb=" CB  ARG C  83 "
        pdb=" CG  ARG C  83 "
      ideal   model   delta    sigma   weight residual
     114.10  119.70   -5.60 2.00e+00 2.50e-01 7.85e+00
  angle pdb=" CA  ARG B  83 "
        pdb=" CB  ARG B  83 "
        pdb=" CG  ARG B  83 "
      ideal   model   delta    sigma   weight residual
     114.10  119.68   -5.58 2.00e+00 2.50e-01 7.77e+00
  angle pdb=" CA  ARG A  83 "
        pdb=" CB  ARG A  83 "
        pdb=" CG  ARG A  83 "
      ideal   model   delta    sigma   weight residual
     114.10  119.65   -5.55 2.00e+00 2.50e-01 7.70e+00
  angle pdb=" CA  ARG B 356 "
        pdb=" CB  ARG B 356 "
        pdb=" CG  ARG B 356 "
      ideal   model   delta    sigma   weight residual
     114.10  118.95   -4.85 2.00e+00 2.50e-01 5.89e+00
  angle pdb=" CA  ARG C 356 "
        pdb=" CB  ARG C 356 "
        pdb=" CG  ARG C 356 "
      ideal   model   delta    sigma   weight residual
     114.10  118.94   -4.84 2.00e+00 2.50e-01 5.85e+00
  ... (remaining 14399 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.43: 5515
       17.43 -    34.86: 510
       34.86 -    52.29: 101
       52.29 -    69.73: 43
       69.73 -    87.16: 26
  Dihedral angle restraints: 6195
    sinusoidal: 2895
      harmonic: 3300
  Sorted by residual:
  dihedral pdb=" CA  HIS B 208 "
           pdb=" C   HIS B 208 "
           pdb=" N   ASP B 209 "
           pdb=" CA  ASP B 209 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.22   16.78     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" CA  HIS A 208 "
           pdb=" C   HIS A 208 "
           pdb=" N   ASP A 209 "
           pdb=" CA  ASP A 209 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.26   16.74     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  HIS C 208 "
           pdb=" C   HIS C 208 "
           pdb=" N   ASP C 209 "
           pdb=" CA  ASP C 209 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.27   16.73     0      5.00e+00 4.00e-02 1.12e+01
  ... (remaining 6192 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1070
       0.028 -    0.056: 388
       0.056 -    0.084: 193
       0.084 -    0.112: 55
       0.112 -    0.140: 16
  Chirality restraints: 1722
  Sorted by residual:
  chirality pdb=" CA  TYR C  65 "
            pdb=" N   TYR C  65 "
            pdb=" C   TYR C  65 "
            pdb=" CB  TYR C  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.89e-01
  chirality pdb=" CA  TYR A  65 "
            pdb=" N   TYR A  65 "
            pdb=" C   TYR A  65 "
            pdb=" CB  TYR A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.73e-01
  chirality pdb=" CA  TYR B  65 "
            pdb=" N   TYR B  65 "
            pdb=" C   TYR B  65 "
            pdb=" CB  TYR B  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 1719 not shown)

  Planarity restraints: 1632
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  13 "    0.032 5.00e-02 4.00e+02   4.93e-02 3.89e+00
        pdb=" N   PRO B  14 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B  14 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B  14 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C  13 "    0.032 5.00e-02 4.00e+02   4.92e-02 3.87e+00
        pdb=" N   PRO C  14 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO C  14 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C  14 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  13 "    0.032 5.00e-02 4.00e+02   4.89e-02 3.82e+00
        pdb=" N   PRO A  14 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A  14 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A  14 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1629 not shown)

  Histogram of nonbonded interaction distances:
        0.01 -     0.99: 1130
        0.99 -     1.97: 2634
        1.97 -     2.95: 9206
        2.95 -     3.92: 36703
        3.92 -     4.90: 62521
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 112194
  Sorted by model distance:
  nonbonded pdb=" C3'   A S  10 "
            pdb=" C3'   A R  16 "
     model   vdw
     0.014 3.900
  nonbonded pdb=" C3'   A S  16 "
            pdb=" C3'   A U  10 "
     model   vdw
     0.014 3.900
  nonbonded pdb=" C5'   G R  17 "
            pdb=" C5'   A U   5 "
     model   vdw
     0.014 3.840
  nonbonded pdb=" O3'   A S  16 "
            pdb=" O3'   A U  10 "
     model   vdw
     0.018 3.040
  nonbonded pdb=" O3'   A S  10 "
            pdb=" O3'   A R  16 "
     model   vdw
     0.018 3.040
  ... (remaining 112189 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.33 max=1.00 mean=0.92
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:             9.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     11.530
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
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      :  0.003   0.039  10450  Z= 0.148
  Angle     :  0.612   7.587  14404  Z= 0.324
  Chirality :  0.038   0.140   1722
  Planarity :  0.005   0.049   1632
  Dihedral  : 15.199  87.158   4059
  Min Nonbonded Distance : 0.014

Molprobity Statistics.
  All-atom Clashscore : 16.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.26), residues: 1125
  helix:  1.57 (0.19), residues: 741
  sheet: -0.91 (0.58), residues: 84
  loop :  0.38 (0.43), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  20 
 TYR   0.025   0.002   TYR A 211 
 PHE   0.013   0.001   PHE B 195 
 TRP   0.012   0.002   TRP A 174 
 HIS   0.004   0.001   HIS C  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (10450)
  covalent geometry    : angle       0.61218 (14404)
  hydrogen bonds       : bond        0.17407 (  651)
  hydrogen bonds       : angle       5.99784 ( 1719)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 382
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  212 ASP cc_start: 0.8488 (m-30) cc_final: 0.8113 (m-30)
REVERT: B  345 GLU cc_start: 0.8411 (mm-30) cc_final: 0.8176 (mm-30)
REVERT: A    2 MET cc_start: 0.8445 (ppp) cc_final: 0.8231 (ppp)
REVERT: A   28 ASP cc_start: 0.8390 (m-30) cc_final: 0.8101 (m-30)
REVERT: A   80 LYS cc_start: 0.8299 (mtmm) cc_final: 0.8061 (mtmm)
REVERT: A  212 ASP cc_start: 0.8360 (m-30) cc_final: 0.7947 (m-30)
REVERT: A  252 ARG cc_start: 0.8079 (mmt90) cc_final: 0.7833 (mmt90)
REVERT: A  257 LYS cc_start: 0.9229 (tppp) cc_final: 0.8923 (mmmm)
REVERT: A  323 TYR cc_start: 0.9059 (m-80) cc_final: 0.8726 (m-80)
REVERT: A  345 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8098 (mm-30)
REVERT: A  380 GLN cc_start: 0.8899 (tp-100) cc_final: 0.8618 (tp40)
REVERT: C   80 LYS cc_start: 0.8386 (mtmm) cc_final: 0.7991 (mtmm)
REVERT: C   87 TYR cc_start: 0.8547 (m-80) cc_final: 0.8289 (m-80)
REVERT: C  180 MET cc_start: 0.8537 (mpp) cc_final: 0.8304 (mpp)
REVERT: C  257 LYS cc_start: 0.9206 (tppp) cc_final: 0.8842 (mmmm)
REVERT: C  275 GLU cc_start: 0.8213 (mp0) cc_final: 0.7988 (mp0)
REVERT: C  292 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7801 (mm-30)
REVERT: C  345 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8071 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 382
  average time/residue: 0.1144
  time to fit residues: 57.3371
Evaluate side-chains
  318 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 318
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B  64 HIS
** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 GLN
A  18 HIS
A  64 HIS
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 344 GLN
C  18 HIS
C  64 HIS
C  74 ASN
** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 380 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.166897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.143015 restraints weight = 19693.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 3.88
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3941 r_free = 0.3941    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3929 r_free = 0.3929    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.7384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.019   0.320  10450  Z= 1.112
  Angle     :  3.850  74.710  14404  Z= 1.701
  Chirality :  0.332   4.727   1722
  Planarity :  0.011   0.132   1632
  Dihedral  : 20.536 169.991   1932
  Min Nonbonded Distance : 1.583

Molprobity Statistics.
  All-atom Clashscore : 43.41
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.38 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 16.21 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.25), residues: 1125
  helix:  1.11 (0.19), residues: 717
  sheet: -1.94 (0.85), residues: 30
  loop : -1.16 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.002   ARG C 157 
 TYR   0.037   0.003   TYR B 211 
 PHE   0.026   0.002   PHE C 184 
 TRP   0.009   0.002   TRP A 174 
 HIS   0.013   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.01887 (10450)
  covalent geometry    : angle       3.85038 (14404)
  hydrogen bonds       : bond        0.61022 (  651)
  hydrogen bonds       : angle       5.58883 ( 1719)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  407 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 374
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.6397 (m-80) cc_final: 0.6017 (m-80)
REVERT: B   80 LYS cc_start: 0.8474 (mtmm) cc_final: 0.8176 (mtmm)
REVERT: B   88 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8031 (mm-30)
REVERT: B  153 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8254 (mm-30)
REVERT: B  198 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9000 (mp)
REVERT: B  212 ASP cc_start: 0.8548 (m-30) cc_final: 0.8199 (m-30)
REVERT: B  345 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8253 (mm-30)
REVERT: B  357 LYS cc_start: 0.8766 (mtmm) cc_final: 0.8194 (mtmt)
REVERT: B  383 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8200 (tm-30)
REVERT: A   47 ILE cc_start: 0.9157 (mm) cc_final: 0.8871 (mp)
REVERT: A   71 ASP cc_start: 0.8186 (t0) cc_final: 0.7894 (t0)
REVERT: A   80 LYS cc_start: 0.8406 (mtmm) cc_final: 0.7974 (mtmm)
REVERT: A   81 TYR cc_start: 0.8505 (t80) cc_final: 0.8125 (t80)
REVERT: A   84 ASP cc_start: 0.8012 (m-30) cc_final: 0.7722 (m-30)
REVERT: A  198 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.8975 (mp)
REVERT: A  252 ARG cc_start: 0.8170 (mmt90) cc_final: 0.7862 (mmt90)
REVERT: A  288 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8244 (tp)
REVERT: A  308 THR cc_start: 0.7453 (m) cc_final: 0.6982 (m)
REVERT: A  322 GLN cc_start: 0.9125 (pm20) cc_final: 0.8831 (pm20)
REVERT: A  323 TYR cc_start: 0.8891 (m-80) cc_final: 0.8452 (m-80)
REVERT: A  324 GLN cc_start: 0.8421 (mt0) cc_final: 0.8204 (mm-40)
REVERT: A  325 GLN cc_start: 0.8500 (mp10) cc_final: 0.8233 (mp10)
REVERT: A  342 GLU cc_start: 0.8192 (pp20) cc_final: 0.7828 (pp20)
REVERT: A  345 GLU cc_start: 0.8526 (mm-30) cc_final: 0.8189 (mm-30)
REVERT: A  356 ARG cc_start: 0.7538 (mmt-90) cc_final: 0.7205 (mmt-90)
REVERT: A  368 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8654 (tm-30)
REVERT: A  383 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7910 (tm-30)
REVERT: C   27 PHE cc_start: 0.8599 (m-10) cc_final: 0.8236 (m-10)
REVERT: C   32 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8548 (tp-100)
REVERT: C   65 TYR cc_start: 0.6401 (m-10) cc_final: 0.6189 (m-80)
REVERT: C  148 ASP cc_start: 0.7350 (p0) cc_final: 0.7148 (p0)
REVERT: C  180 MET cc_start: 0.8655 (mpp) cc_final: 0.8371 (mpp)
REVERT: C  198 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9060 (mp)
REVERT: C  252 ARG cc_start: 0.8207 (mmt90) cc_final: 0.7893 (mmt90)
REVERT: C  275 GLU cc_start: 0.8340 (mp0) cc_final: 0.8125 (mp0)
REVERT: C  325 GLN cc_start: 0.8716 (mp10) cc_final: 0.8452 (mp10)
REVERT: C  345 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8248 (mm-30)
REVERT: C  356 ARG cc_start: 0.7523 (mmt-90) cc_final: 0.6965 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8995 (mtmm) cc_final: 0.8392 (mtmm)
REVERT: C  380 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8424 (tp40)
REVERT: C  382 ARG cc_start: 0.8410 (mmp80) cc_final: 0.7995 (mmp-170)
REVERT: C  383 GLU cc_start: 0.8354 (tm-30) cc_final: 0.8076 (tm-30)
  outliers start: 33
  outliers final: 15
  residues processed: 393
  average time/residue: 0.1248
  time to fit residues: 64.8524
Evaluate side-chains
  361 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 341
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue  144 LEU
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  217 ASN
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  317 VAL
Chi-restraints excluded: chain C residue  319 VAL
Chi-restraints excluded: chain C residue  380 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 78 optimal weight:    9.9990
   chunk 113 optimal weight:    5.9990
   chunk 67 optimal weight:    0.8980
   chunk 14 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 101 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0570
   chunk 108 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 344 GLN
A  32 GLN
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 310 HIS
C  64 HIS
** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 344 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.172798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.147938 restraints weight = 19510.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.4020 rms_B_bonded: 3.89
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4020 r_free = 0.4020    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4016 r_free = 0.4016    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.9375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.201  10450  Z= 0.682
  Angle     :  2.645  70.275  14404  Z= 1.185
  Chirality :  0.316   4.646   1722
  Planarity :  0.008   0.093   1632
  Dihedral  : 20.931 178.875   1932
  Min Nonbonded Distance : 1.739

Molprobity Statistics.
  All-atom Clashscore : 42.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 18.14 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.25), residues: 1125
  helix:  1.19 (0.19), residues: 717
  sheet: -2.35 (0.87), residues: 30
  loop : -1.27 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 327 
 TYR   0.032   0.002   TYR C 323 
 PHE   0.029   0.002   PHE C 184 
 TRP   0.008   0.001   TRP A 174 
 HIS   0.008   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.01186 (10450)
  covalent geometry    : angle       2.64512 (14404)
  hydrogen bonds       : bond        0.56273 (  651)
  hydrogen bonds       : angle       5.11300 ( 1719)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  445 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 392
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.6494 (m-80) cc_final: 0.6227 (m-80)
REVERT: B   80 LYS cc_start: 0.8482 (mtmm) cc_final: 0.8092 (mtmm)
REVERT: B   88 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7886 (mm-30)
REVERT: B  133 PHE cc_start: 0.8636 (t80) cc_final: 0.8388 (t80)
REVERT: B  134 LEU cc_start: 0.9263 (mt) cc_final: 0.8815 (mt)
REVERT: B  148 ASP cc_start: 0.6788 (p0) cc_final: 0.6305 (p0)
REVERT: B  152 ILE cc_start: 0.8720 (pt) cc_final: 0.8500 (pt)
REVERT: B  153 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7589 (mm-30)
REVERT: B  180 MET cc_start: 0.8786 (mpp) cc_final: 0.8580 (mpp)
REVERT: B  198 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9018 (mp)
REVERT: B  252 ARG cc_start: 0.8110 (mmt90) cc_final: 0.7819 (mmt90)
REVERT: B  259 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7871 (mm-30)
REVERT: B  308 THR cc_start: 0.7262 (m) cc_final: 0.6719 (m)
REVERT: B  319 VAL cc_start: 0.3423 (OUTLIER) cc_final: 0.3152 (t)
REVERT: B  323 TYR cc_start: 0.8559 (m-80) cc_final: 0.8090 (m-10)
REVERT: B  345 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8274 (mm-30)
REVERT: B  354 GLU cc_start: 0.8850 (tp30) cc_final: 0.8295 (tp30)
REVERT: B  356 ARG cc_start: 0.7710 (mmt-90) cc_final: 0.7281 (mmt-90)
REVERT: B  357 LYS cc_start: 0.8910 (mtmm) cc_final: 0.8573 (mtmm)
REVERT: B  383 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8318 (tm-30)
REVERT: A    2 MET cc_start: 0.8484 (ppp) cc_final: 0.8208 (ppp)
REVERT: A   40 ILE cc_start: 0.9176 (mt) cc_final: 0.8938 (mt)
REVERT: A   44 ASN cc_start: 0.9074 (p0) cc_final: 0.8631 (p0)
REVERT: A   65 TYR cc_start: 0.5681 (m-80) cc_final: 0.5077 (m-80)
REVERT: A   80 LYS cc_start: 0.8372 (mtmm) cc_final: 0.7781 (mtmm)
REVERT: A   81 TYR cc_start: 0.8541 (t80) cc_final: 0.8302 (t80)
REVERT: A   84 ASP cc_start: 0.7943 (m-30) cc_final: 0.7672 (m-30)
REVERT: A   88 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7915 (mm-30)
REVERT: A  157 ARG cc_start: 0.8560 (ttm170) cc_final: 0.8352 (ttp80)
REVERT: A  198 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9021 (mp)
REVERT: A  288 ILE cc_start: 0.8529 (tp) cc_final: 0.8126 (tp)
REVERT: A  290 ASN cc_start: 0.8499 (m-40) cc_final: 0.8268 (m-40)
REVERT: A  295 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7543 (mp)
REVERT: A  308 THR cc_start: 0.7992 (m) cc_final: 0.6777 (m)
REVERT: A  337 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8844 (mm)
REVERT: A  345 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8228 (mm-30)
REVERT: A  354 GLU cc_start: 0.8747 (tp30) cc_final: 0.8510 (pt0)
REVERT: A  356 ARG cc_start: 0.7524 (mmt-90) cc_final: 0.6980 (mmt-90)
REVERT: A  368 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8639 (tm-30)
REVERT: A  383 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8006 (tm-30)
REVERT: A  385 LEU cc_start: 0.8811 (mt) cc_final: 0.8562 (mt)
REVERT: C   27 PHE cc_start: 0.8483 (m-10) cc_final: 0.8257 (m-10)
REVERT: C   32 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8528 (tp-100)
REVERT: C   37 ASN cc_start: 0.9138 (m-40) cc_final: 0.8917 (m-40)
REVERT: C   64 HIS cc_start: 0.8737 (t-90) cc_final: 0.8463 (t-90)
REVERT: C   72 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8783 (mmmt)
REVERT: C   80 LYS cc_start: 0.8479 (mtmm) cc_final: 0.7973 (mtmm)
REVERT: C  152 ILE cc_start: 0.8773 (pt) cc_final: 0.8565 (pt)
REVERT: C  157 ARG cc_start: 0.7616 (ttm110) cc_final: 0.7217 (ttp-170)
REVERT: C  198 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9031 (mp)
REVERT: C  234 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9156 (mm)
REVERT: C  247 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8682 (tp)
REVERT: C  252 ARG cc_start: 0.8120 (mmt90) cc_final: 0.7811 (mmt90)
REVERT: C  308 THR cc_start: 0.8102 (m) cc_final: 0.7870 (m)
REVERT: C  345 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8235 (mm-30)
REVERT: C  356 ARG cc_start: 0.7506 (mmt-90) cc_final: 0.6776 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8912 (mtmm) cc_final: 0.8358 (mtmm)
REVERT: C  381 LYS cc_start: 0.6990 (ttpt) cc_final: 0.6535 (ttpt)
REVERT: C  383 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8106 (tm-30)
  outliers start: 53
  outliers final: 19
  residues processed: 419
  average time/residue: 0.1215
  time to fit residues: 67.8546
Evaluate side-chains
  383 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 355
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  361 GLN
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  247 LEU
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  374 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 113 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 101 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
B  18 HIS
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 289 ASN
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 GLN
B 380 GLN
A 371 HIS
C  21 ASN
C 293 HIS
** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.173370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.147447 restraints weight = 19581.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3999 rms_B_bonded: 3.99
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3999
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3999 r_free = 0.3999    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3994 r_free = 0.3994    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3994
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          1.0215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.207  10450  Z= 0.590
  Angle     :  2.380  70.232  14404  Z= 1.054
  Chirality :  0.298   4.609   1722
  Planarity :  0.007   0.084   1632
  Dihedral  : 22.106 172.896   1932
  Min Nonbonded Distance : 1.756

Molprobity Statistics.
  All-atom Clashscore : 38.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 22.73 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.25), residues: 1125
  helix:  1.17 (0.19), residues: 717
  sheet: -2.51 (0.82), residues: 30
  loop : -1.12 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 327 
 TYR   0.031   0.002   TYR A 323 
 PHE   0.023   0.002   PHE C 184 
 TRP   0.007   0.001   TRP A 174 
 HIS   0.006   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.01046 (10450)
  covalent geometry    : angle       2.37965 (14404)
  hydrogen bonds       : bond        0.49625 (  651)
  hydrogen bonds       : angle       5.09110 ( 1719)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  439 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 382
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.6755 (m-80) cc_final: 0.6326 (m-80)
REVERT: B   83 ARG cc_start: 0.8106 (mmp-170) cc_final: 0.7893 (mmp-170)
REVERT: B   88 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7815 (mm-30)
REVERT: B  148 ASP cc_start: 0.6470 (p0) cc_final: 0.5834 (p0)
REVERT: B  173 HIS cc_start: 0.7747 (t-90) cc_final: 0.7492 (t-90)
REVERT: B  180 MET cc_start: 0.8836 (mpp) cc_final: 0.8552 (mpp)
REVERT: B  198 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9097 (mp)
REVERT: B  259 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7983 (mm-30)
REVERT: B  295 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7347 (mp)
REVERT: B  331 HIS cc_start: 0.6827 (t70) cc_final: 0.6501 (t70)
REVERT: B  345 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8389 (mm-30)
REVERT: B  357 LYS cc_start: 0.9000 (mtmm) cc_final: 0.8685 (mtmm)
REVERT: B  365 GLN cc_start: 0.8784 (tp40) cc_final: 0.8455 (tp-100)
REVERT: B  382 ARG cc_start: 0.8422 (mmp80) cc_final: 0.8208 (mmp-170)
REVERT: B  383 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8279 (tm-30)
REVERT: A   44 ASN cc_start: 0.9101 (p0) cc_final: 0.8596 (p0)
REVERT: A   47 ILE cc_start: 0.9026 (mm) cc_final: 0.8821 (mp)
REVERT: A   80 LYS cc_start: 0.8387 (mtmm) cc_final: 0.7938 (mtmm)
REVERT: A   84 ASP cc_start: 0.7953 (m-30) cc_final: 0.7682 (m-30)
REVERT: A  198 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9078 (mp)
REVERT: A  257 LYS cc_start: 0.9034 (tppp) cc_final: 0.8637 (mmmm)
REVERT: A  259 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8173 (mm-30)
REVERT: A  327 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7407 (ttp-170)
REVERT: A  337 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8995 (mm)
REVERT: A  345 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8207 (mm-30)
REVERT: A  354 GLU cc_start: 0.8437 (tp30) cc_final: 0.8030 (tt0)
REVERT: A  356 ARG cc_start: 0.7623 (mmt-90) cc_final: 0.7000 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8690 (pttp) cc_final: 0.8253 (ptpp)
REVERT: A  368 GLU cc_start: 0.8829 (tm-30) cc_final: 0.8559 (tm-30)
REVERT: A  371 HIS cc_start: 0.8504 (t70) cc_final: 0.8228 (t70)
REVERT: A  382 ARG cc_start: 0.8441 (tpp-160) cc_final: 0.8178 (mmp80)
REVERT: A  383 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: A  385 LEU cc_start: 0.8669 (mt) cc_final: 0.8254 (mt)
REVERT: C   27 PHE cc_start: 0.8388 (m-10) cc_final: 0.8175 (m-10)
REVERT: C   32 GLN cc_start: 0.8789 (tp-100) cc_final: 0.8528 (tp-100)
REVERT: C   47 ILE cc_start: 0.9182 (mm) cc_final: 0.8838 (mp)
REVERT: C   64 HIS cc_start: 0.8616 (t-90) cc_final: 0.8166 (t-90)
REVERT: C   65 TYR cc_start: 0.6508 (m-80) cc_final: 0.6183 (m-80)
REVERT: C   80 LYS cc_start: 0.8481 (mtmm) cc_final: 0.7779 (mtmm)
REVERT: C   84 ASP cc_start: 0.8140 (m-30) cc_final: 0.7856 (m-30)
REVERT: C  145 VAL cc_start: 0.3618 (OUTLIER) cc_final: 0.2282 (t)
REVERT: C  173 HIS cc_start: 0.8051 (t-90) cc_final: 0.7795 (t-90)
REVERT: C  180 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8480 (mpp)
REVERT: C  198 ILE cc_start: 0.9427 (OUTLIER) cc_final: 0.9133 (mp)
REVERT: C  234 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9161 (mm)
REVERT: C  247 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8783 (tp)
REVERT: C  252 ARG cc_start: 0.8323 (mmt90) cc_final: 0.7887 (mmt90)
REVERT: C  308 THR cc_start: 0.8059 (m) cc_final: 0.7831 (m)
REVERT: C  345 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8269 (mm-30)
REVERT: C  356 ARG cc_start: 0.7549 (mmt-90) cc_final: 0.7121 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8324 (mtmm)
REVERT: C  365 GLN cc_start: 0.8875 (tp40) cc_final: 0.8551 (tp-100)
REVERT: C  383 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8202 (tm-30)
  outliers start: 57
  outliers final: 30
  residues processed: 407
  average time/residue: 0.1245
  time to fit residues: 67.4707
Evaluate side-chains
  383 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 344
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  361 GLN
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain A residue   30 ASN
Chi-restraints excluded: chain A residue   31 HIS
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  145 VAL
Chi-restraints excluded: chain C residue  165 GLN
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  180 MET
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  216 SER
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  247 LEU
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  314 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 9 optimal weight:    8.9990
   chunk 21 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 103 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 GLN
** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 284 ASN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.175209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.150161 restraints weight = 19543.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.4026 rms_B_bonded: 3.85
r_work (final): 0.4026
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4027 r_free = 0.4027    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4025 r_free = 0.4025    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4025
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          1.0951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.203  10450  Z= 0.536
  Angle     :  2.264  70.570  14404  Z= 0.993
  Chirality :  0.270   4.643   1722
  Planarity :  0.007   0.094   1632
  Dihedral  : 22.287 177.658   1932
  Min Nonbonded Distance : 1.754

Molprobity Statistics.
  All-atom Clashscore : 37.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 24.36 %
    Favored  : 69.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.25), residues: 1125
  helix:  1.21 (0.19), residues: 720
  sheet: -2.50 (0.81), residues: 30
  loop : -1.06 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 157 
 TYR   0.020   0.002   TYR A 323 
 PHE   0.032   0.002   PHE B 184 
 TRP   0.008   0.001   TRP A 174 
 HIS   0.007   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00962 (10450)
  covalent geometry    : angle       2.26357 (14404)
  hydrogen bonds       : bond        0.49099 (  651)
  hydrogen bonds       : angle       5.11396 ( 1719)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  444 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 388
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.6582 (m-80) cc_final: 0.6051 (m-80)
REVERT: B   80 LYS cc_start: 0.8504 (mtmm) cc_final: 0.8147 (mtmm)
REVERT: B   88 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7855 (mm-30)
REVERT: B  134 LEU cc_start: 0.9225 (mt) cc_final: 0.8561 (mt)
REVERT: B  148 ASP cc_start: 0.6449 (p0) cc_final: 0.5827 (p0)
REVERT: B  149 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7468 (mmm-85)
REVERT: B  173 HIS cc_start: 0.7690 (t-90) cc_final: 0.7343 (t-90)
REVERT: B  198 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9056 (mp)
REVERT: B  247 LEU cc_start: 0.8846 (tp) cc_final: 0.8640 (tp)
REVERT: B  257 LYS cc_start: 0.9016 (tppp) cc_final: 0.8772 (mmtp)
REVERT: B  334 GLU cc_start: 0.8768 (tp30) cc_final: 0.8536 (tp30)
REVERT: B  355 GLU cc_start: 0.8529 (pm20) cc_final: 0.8043 (pm20)
REVERT: B  357 LYS cc_start: 0.9062 (mtmm) cc_final: 0.8738 (mtmm)
REVERT: B  365 GLN cc_start: 0.8788 (tp40) cc_final: 0.8567 (tp40)
REVERT: B  382 ARG cc_start: 0.8427 (mmp80) cc_final: 0.8184 (mmt180)
REVERT: B  383 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8262 (tm-30)
REVERT: A   64 HIS cc_start: 0.8517 (t-90) cc_final: 0.8310 (t-90)
REVERT: A   80 LYS cc_start: 0.8368 (mtmm) cc_final: 0.7928 (mtmm)
REVERT: A   84 ASP cc_start: 0.7962 (m-30) cc_final: 0.7693 (m-30)
REVERT: A  149 ARG cc_start: 0.6871 (mmm160) cc_final: 0.6484 (mmm160)
REVERT: A  153 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7393 (mm-30)
REVERT: A  198 ILE cc_start: 0.9305 (OUTLIER) cc_final: 0.9087 (mp)
REVERT: A  337 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9032 (mm)
REVERT: A  345 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8203 (mm-30)
REVERT: A  354 GLU cc_start: 0.8371 (tp30) cc_final: 0.7861 (tt0)
REVERT: A  356 ARG cc_start: 0.7706 (mmt-90) cc_final: 0.7228 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8620 (pttp) cc_final: 0.8190 (ptpp)
REVERT: A  383 GLU cc_start: 0.8605 (tm-30) cc_final: 0.7984 (tm-30)
REVERT: A  387 ARG cc_start: 0.8690 (ptp90) cc_final: 0.8306 (ptp90)
REVERT: C   32 GLN cc_start: 0.8770 (tp-100) cc_final: 0.8501 (tp-100)
REVERT: C   33 VAL cc_start: 0.8818 (m) cc_final: 0.8414 (m)
REVERT: C   37 ASN cc_start: 0.9208 (m-40) cc_final: 0.8960 (m-40)
REVERT: C   64 HIS cc_start: 0.8547 (t-90) cc_final: 0.8267 (t-90)
REVERT: C   65 TYR cc_start: 0.6522 (m-80) cc_final: 0.6201 (m-80)
REVERT: C   87 TYR cc_start: 0.8814 (m-80) cc_final: 0.8559 (m-80)
REVERT: C  180 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8426 (mpp)
REVERT: C  194 LYS cc_start: 0.8624 (mttm) cc_final: 0.8408 (mttm)
REVERT: C  198 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9066 (mp)
REVERT: C  252 ARG cc_start: 0.8329 (mmt90) cc_final: 0.8053 (mmt90)
REVERT: C  308 THR cc_start: 0.7722 (m) cc_final: 0.7206 (m)
REVERT: C  324 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6729 (mm-40)
REVERT: C  356 ARG cc_start: 0.7600 (mmt-90) cc_final: 0.7121 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8763 (mtmm) cc_final: 0.8315 (mtmm)
REVERT: C  365 GLN cc_start: 0.8845 (tp40) cc_final: 0.8273 (tp-100)
REVERT: C  368 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8083 (tm-30)
REVERT: C  383 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8315 (tm-30)
  outliers start: 56
  outliers final: 30
  residues processed: 411
  average time/residue: 0.1192
  time to fit residues: 64.6659
Evaluate side-chains
  371 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 336
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   48 ASP
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  361 GLN
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain C residue   23 LYS
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  165 GLN
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  180 MET
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  204 LEU
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  257 LYS
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  354 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 54 optimal weight:    7.9990
   chunk 77 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   chunk 115 optimal weight:    6.9990
   chunk 19 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0050
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 217 ASN
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 318 ASN
A 380 GLN
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 284 ASN
** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.181691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.155217 restraints weight = 19694.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.4095 rms_B_bonded: 4.12
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4091 r_free = 0.4091    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4089 r_free = 0.4089    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4089
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          1.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.197  10450  Z= 0.510
  Angle     :  2.140  71.282  14404  Z= 0.942
  Chirality :  0.262   4.558   1722
  Planarity :  0.007   0.126   1632
  Dihedral  : 21.782 167.820   1932
  Min Nonbonded Distance : 1.744

Molprobity Statistics.
  All-atom Clashscore : 36.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 25.48 %
    Favored  : 68.20 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.25), residues: 1125
  helix:  0.79 (0.19), residues: 738
  sheet: -2.74 (0.77), residues: 30
  loop : -0.76 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  83 
 TYR   0.022   0.002   TYR A 211 
 PHE   0.038   0.003   PHE A 184 
 TRP   0.008   0.001   TRP A 174 
 HIS   0.013   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00926 (10450)
  covalent geometry    : angle       2.13972 (14404)
  hydrogen bonds       : bond        0.46172 (  651)
  hydrogen bonds       : angle       5.17693 ( 1719)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  427 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 365
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7282 (mt-10)
REVERT: B   65 TYR cc_start: 0.6559 (m-80) cc_final: 0.5997 (m-80)
REVERT: B   80 LYS cc_start: 0.8426 (mtmm) cc_final: 0.8016 (mtmm)
REVERT: B   81 TYR cc_start: 0.8265 (t80) cc_final: 0.8046 (t80)
REVERT: B   88 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7807 (mm-30)
REVERT: B  110 TYR cc_start: 0.7318 (m-80) cc_final: 0.7001 (m-10)
REVERT: B  134 LEU cc_start: 0.9005 (mt) cc_final: 0.8476 (mt)
REVERT: B  180 MET cc_start: 0.8864 (mpp) cc_final: 0.8174 (mpp)
REVERT: B  198 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9031 (mp)
REVERT: B  257 LYS cc_start: 0.9017 (tppp) cc_final: 0.8647 (mmtp)
REVERT: B  332 ASP cc_start: 0.8476 (m-30) cc_final: 0.8146 (m-30)
REVERT: B  345 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7908 (mm-30)
REVERT: B  357 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8776 (mtmt)
REVERT: B  365 GLN cc_start: 0.8670 (tp40) cc_final: 0.8312 (tp40)
REVERT: B  368 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8256 (tm-30)
REVERT: A   80 LYS cc_start: 0.8387 (mtmm) cc_final: 0.7892 (mtmm)
REVERT: A   84 ASP cc_start: 0.8003 (m-30) cc_final: 0.7712 (m-30)
REVERT: A  337 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9008 (mm)
REVERT: A  345 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8261 (mm-30)
REVERT: A  354 GLU cc_start: 0.8394 (tp30) cc_final: 0.7901 (tt0)
REVERT: A  356 ARG cc_start: 0.7671 (mmt-90) cc_final: 0.6910 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8571 (pttp) cc_final: 0.7992 (ptpp)
REVERT: A  360 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7776 (mt-10)
REVERT: A  383 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8417 (tm-30)
REVERT: A  385 LEU cc_start: 0.8202 (mm) cc_final: 0.7886 (mm)
REVERT: C    3 ASP cc_start: 0.8423 (t0) cc_final: 0.8166 (t0)
REVERT: C   33 VAL cc_start: 0.8828 (m) cc_final: 0.8433 (m)
REVERT: C   37 ASN cc_start: 0.9220 (m-40) cc_final: 0.8993 (m-40)
REVERT: C   47 ILE cc_start: 0.9192 (mm) cc_final: 0.8895 (mp)
REVERT: C   64 HIS cc_start: 0.8538 (t-90) cc_final: 0.8198 (t-90)
REVERT: C   65 TYR cc_start: 0.6632 (m-80) cc_final: 0.6240 (m-80)
REVERT: C   80 LYS cc_start: 0.8420 (mtmm) cc_final: 0.7797 (mtmm)
REVERT: C   84 ASP cc_start: 0.8272 (m-30) cc_final: 0.7958 (m-30)
REVERT: C   87 TYR cc_start: 0.8790 (m-80) cc_final: 0.8589 (m-80)
REVERT: C  173 HIS cc_start: 0.8003 (t-90) cc_final: 0.7798 (t-90)
REVERT: C  180 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8300 (mpp)
REVERT: C  198 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9071 (mp)
REVERT: C  257 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8906 (mmmm)
REVERT: C  281 ARG cc_start: 0.8621 (tpp-160) cc_final: 0.8303 (tpp80)
REVERT: C  357 LYS cc_start: 0.8710 (mtmm) cc_final: 0.8000 (mtmm)
REVERT: C  360 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8047 (mt-10)
REVERT: C  365 GLN cc_start: 0.8877 (tp40) cc_final: 0.8373 (tp-100)
REVERT: C  368 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8128 (tm-30)
REVERT: C  382 ARG cc_start: 0.8524 (mmp80) cc_final: 0.8134 (mmp-170)
REVERT: C  383 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8264 (tm-30)
  outliers start: 62
  outliers final: 34
  residues processed: 393
  average time/residue: 0.1204
  time to fit residues: 63.7328
Evaluate side-chains
  381 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 342
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  275 GLU
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  346 ILE
Chi-restraints excluded: chain B residue  361 GLN
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   30 ASN
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  209 ASP
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain A residue  380 GLN
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  180 MET
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  216 SER
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  257 LYS
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  323 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 4 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 70 optimal weight:    8.9990
   chunk 27 optimal weight:    0.7980
   chunk 115 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 114 optimal weight:    5.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 GLN
A 380 GLN
C  32 GLN
C 284 ASN
C 338 GLN
** C 347 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 = 0.4397 r_free = 0.4397 target = 0.181501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.155509 restraints weight = 19326.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.4098 rms_B_bonded: 4.08
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4098
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4098 r_free = 0.4098    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4098 r_free = 0.4098    target_work(ls_wunit_k1) = 0.155         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4098
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          1.2288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.193  10450  Z= 0.492
  Angle     :  2.144  72.306  14404  Z= 0.936
  Chirality :  0.229   4.493   1722
  Planarity :  0.007   0.078   1632
  Dihedral  : 21.657 166.137   1932
  Min Nonbonded Distance : 1.754

Molprobity Statistics.
  All-atom Clashscore : 36.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 27.83 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.26), residues: 1125
  helix:  0.61 (0.19), residues: 753
  sheet: -1.82 (0.53), residues: 72
  loop : -0.40 (0.40), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 327 
 TYR   0.020   0.002   TYR C 211 
 PHE   0.033   0.002   PHE B 184 
 TRP   0.007   0.001   TRP B 174 
 HIS   0.008   0.001   HIS C 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00897 (10450)
  covalent geometry    : angle       2.14420 (14404)
  hydrogen bonds       : bond        0.44709 (  651)
  hydrogen bonds       : angle       5.25721 ( 1719)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  401 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 353
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7321 (mt-10)
REVERT: B   27 PHE cc_start: 0.6413 (m-10) cc_final: 0.6151 (m-80)
REVERT: B   65 TYR cc_start: 0.6547 (m-80) cc_final: 0.5943 (m-80)
REVERT: B   80 LYS cc_start: 0.8455 (mtmm) cc_final: 0.8063 (mtmm)
REVERT: B   88 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7801 (mm-30)
REVERT: B  134 LEU cc_start: 0.8962 (mt) cc_final: 0.8405 (mt)
REVERT: B  180 MET cc_start: 0.8818 (mpp) cc_final: 0.8174 (mpp)
REVERT: B  194 LYS cc_start: 0.8806 (mttm) cc_final: 0.8579 (mttm)
REVERT: B  198 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9067 (mp)
REVERT: B  257 LYS cc_start: 0.9045 (tppp) cc_final: 0.8729 (mmtp)
REVERT: B  345 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7655 (mm-30)
REVERT: B  352 ASP cc_start: 0.8624 (p0) cc_final: 0.8253 (p0)
REVERT: B  357 LYS cc_start: 0.9030 (mtmm) cc_final: 0.8685 (mtmm)
REVERT: B  365 GLN cc_start: 0.8612 (tp40) cc_final: 0.8263 (tp40)
REVERT: B  368 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8375 (tm-30)
REVERT: A    3 ASP cc_start: 0.8915 (t0) cc_final: 0.8613 (t0)
REVERT: A   80 LYS cc_start: 0.8355 (mtmm) cc_final: 0.8072 (mmmt)
REVERT: A   84 ASP cc_start: 0.7973 (m-30) cc_final: 0.7700 (m-30)
REVERT: A  252 ARG cc_start: 0.8150 (mmt90) cc_final: 0.7942 (mmt90)
REVERT: A  284 ASN cc_start: 0.8219 (m110) cc_final: 0.7885 (m-40)
REVERT: A  337 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9011 (mm)
REVERT: A  345 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8315 (mm-30)
REVERT: A  354 GLU cc_start: 0.8429 (tp30) cc_final: 0.7903 (tt0)
REVERT: A  356 ARG cc_start: 0.7794 (mmt-90) cc_final: 0.7054 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8562 (pttp) cc_final: 0.7970 (ptpp)
REVERT: A  360 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7841 (mt-10)
REVERT: A  383 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8281 (tm-30)
REVERT: C    3 ASP cc_start: 0.8472 (t0) cc_final: 0.8165 (t0)
REVERT: C   33 VAL cc_start: 0.8852 (m) cc_final: 0.8426 (m)
REVERT: C   37 ASN cc_start: 0.9261 (m-40) cc_final: 0.9034 (m-40)
REVERT: C   47 ILE cc_start: 0.9146 (mm) cc_final: 0.8854 (mp)
REVERT: C   64 HIS cc_start: 0.8524 (t-90) cc_final: 0.8276 (t-90)
REVERT: C   65 TYR cc_start: 0.6624 (m-80) cc_final: 0.6095 (m-80)
REVERT: C   80 LYS cc_start: 0.8454 (mtmm) cc_final: 0.7812 (mtmm)
REVERT: C   84 ASP cc_start: 0.8307 (m-30) cc_final: 0.7999 (m-30)
REVERT: C  134 LEU cc_start: 0.9169 (mt) cc_final: 0.8755 (mt)
REVERT: C  198 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9137 (mp)
REVERT: C  257 LYS cc_start: 0.9153 (mmmm) cc_final: 0.8940 (mmmm)
REVERT: C  281 ARG cc_start: 0.8612 (tpp-160) cc_final: 0.8280 (tpp80)
REVERT: C  336 LYS cc_start: 0.6947 (tttm) cc_final: 0.6739 (ttpp)
REVERT: C  357 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8278 (mtmm)
REVERT: C  365 GLN cc_start: 0.8804 (tp40) cc_final: 0.8336 (tp-100)
REVERT: C  368 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8110 (tm-30)
REVERT: C  383 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8231 (tm-30)
  outliers start: 48
  outliers final: 33
  residues processed: 372
  average time/residue: 0.1202
  time to fit residues: 60.1409
Evaluate side-chains
  352 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 316
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   48 ASP
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  255 LYS
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  346 ILE
Chi-restraints excluded: chain B residue  361 GLN
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   30 ASN
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  139 LEU
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  216 SER
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  378 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   chunk 114 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 115 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 107 optimal weight:    0.2980
   chunk 86 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 HIS
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 179 HIS
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.180309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.154079 restraints weight = 19300.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 4.05
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4062
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4062 r_free = 0.4062    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4063 r_free = 0.4063    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4063
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          1.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.195  10450  Z= 0.480
  Angle     :  2.107  71.389  14404  Z= 0.920
  Chirality :  0.229   4.383   1722
  Planarity :  0.007   0.109   1632
  Dihedral  : 21.685 166.783   1932
  Min Nonbonded Distance : 1.738

Molprobity Statistics.
  All-atom Clashscore : 39.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 29.05 %
    Favored  : 66.46 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.25), residues: 1125
  helix:  0.49 (0.19), residues: 741
  sheet: -1.79 (0.55), residues: 72
  loop : -0.55 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 327 
 TYR   0.023   0.002   TYR A  65 
 PHE   0.037   0.003   PHE C 184 
 TRP   0.011   0.001   TRP C 174 
 HIS   0.009   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00882 (10450)
  covalent geometry    : angle       2.10708 (14404)
  hydrogen bonds       : bond        0.43780 (  651)
  hydrogen bonds       : angle       5.37417 ( 1719)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 342
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7241 (mt-10)
REVERT: B   65 TYR cc_start: 0.6666 (m-80) cc_final: 0.6079 (m-80)
REVERT: B   80 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8044 (mtmm)
REVERT: B   88 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7838 (mm-30)
REVERT: B  134 LEU cc_start: 0.8907 (mt) cc_final: 0.8365 (mt)
REVERT: B  173 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.7609 (m-70)
REVERT: B  180 MET cc_start: 0.8847 (mpp) cc_final: 0.8155 (mpp)
REVERT: B  194 LYS cc_start: 0.8811 (mttm) cc_final: 0.8546 (mttp)
REVERT: B  198 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9079 (mp)
REVERT: B  209 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7579 (p0)
REVERT: B  234 LEU cc_start: 0.9333 (mm) cc_final: 0.9079 (mm)
REVERT: B  257 LYS cc_start: 0.9002 (tppp) cc_final: 0.8780 (mmtp)
REVERT: B  276 TYR cc_start: 0.8917 (m-80) cc_final: 0.8664 (m-80)
REVERT: B  334 GLU cc_start: 0.8707 (tp30) cc_final: 0.8479 (tp30)
REVERT: B  345 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7706 (mm-30)
REVERT: B  357 LYS cc_start: 0.9055 (mtmm) cc_final: 0.8312 (mtmt)
REVERT: B  365 GLN cc_start: 0.8677 (tp40) cc_final: 0.8294 (tp40)
REVERT: B  368 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8404 (tm-30)
REVERT: A   80 LYS cc_start: 0.8299 (mtmm) cc_final: 0.7817 (mtmm)
REVERT: A   84 ASP cc_start: 0.7983 (m-30) cc_final: 0.7688 (m-30)
REVERT: A  281 ARG cc_start: 0.7513 (tpt-90) cc_final: 0.7057 (tpp-160)
REVERT: A  337 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8994 (mm)
REVERT: A  345 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8317 (mm-30)
REVERT: A  354 GLU cc_start: 0.8470 (tp30) cc_final: 0.7970 (tt0)
REVERT: A  356 ARG cc_start: 0.7805 (mmt-90) cc_final: 0.7165 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8587 (pttp) cc_final: 0.8036 (ptpp)
REVERT: A  360 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7934 (mt-10)
REVERT: A  368 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8080 (tm-30)
REVERT: A  388 LEU cc_start: 0.8861 (mm) cc_final: 0.8521 (mm)
REVERT: C    3 ASP cc_start: 0.8576 (t0) cc_final: 0.8317 (t0)
REVERT: C   33 VAL cc_start: 0.8828 (m) cc_final: 0.8387 (m)
REVERT: C   37 ASN cc_start: 0.9267 (m-40) cc_final: 0.9022 (m-40)
REVERT: C   47 ILE cc_start: 0.9151 (mm) cc_final: 0.8920 (mp)
REVERT: C   64 HIS cc_start: 0.8682 (t-90) cc_final: 0.8417 (t-90)
REVERT: C   65 TYR cc_start: 0.6706 (m-80) cc_final: 0.6247 (m-80)
REVERT: C   80 LYS cc_start: 0.8483 (mtmm) cc_final: 0.7866 (mtmm)
REVERT: C   84 ASP cc_start: 0.8348 (m-30) cc_final: 0.8013 (m-30)
REVERT: C  198 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9159 (mp)
REVERT: C  257 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8974 (mmmm)
REVERT: C  281 ARG cc_start: 0.8591 (tpp-160) cc_final: 0.8298 (tpp80)
REVERT: C  356 ARG cc_start: 0.7654 (mmt-90) cc_final: 0.6995 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8438 (mtmm)
REVERT: C  365 GLN cc_start: 0.8830 (tp40) cc_final: 0.8322 (tp-100)
REVERT: C  368 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8164 (tm-30)
REVERT: C  383 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8379 (tm-30)
  outliers start: 44
  outliers final: 30
  residues processed: 362
  average time/residue: 0.1282
  time to fit residues: 61.5906
Evaluate side-chains
  359 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 323
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  209 ASP
Chi-restraints excluded: chain B residue  255 LYS
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  346 ILE
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   30 ASN
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue   31 HIS
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  257 LYS
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  378 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    8.9990
   chunk 51 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 GLN
C  74 ASN
** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.180291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.153545 restraints weight = 19519.169|
|-----------------------------------------------------------------------------|
r_work (start): 0.4077 rms_B_bonded: 4.02
r_work (final): 0.4077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4077
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4077 r_free = 0.4077    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4077 r_free = 0.4077    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4077
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          1.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.194  10450  Z= 0.487
  Angle     :  2.110  71.359  14404  Z= 0.922
  Chirality :  0.224   4.308   1722
  Planarity :  0.007   0.099   1632
  Dihedral  : 21.793 168.181   1932
  Min Nonbonded Distance : 1.736

Molprobity Statistics.
  All-atom Clashscore : 41.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 31.19 %
    Favored  : 64.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.25), residues: 1125
  helix:  0.35 (0.19), residues: 738
  sheet: -1.76 (0.56), residues: 72
  loop : -0.47 (0.38), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 327 
 TYR   0.023   0.002   TYR A  65 
 PHE   0.061   0.003   PHE C 184 
 TRP   0.008   0.001   TRP C 174 
 HIS   0.005   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00904 (10450)
  covalent geometry    : angle       2.10953 (14404)
  hydrogen bonds       : bond        0.43189 (  651)
  hydrogen bonds       : angle       5.49184 ( 1719)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 323
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7050 (mt-10)
REVERT: B   65 TYR cc_start: 0.6550 (m-80) cc_final: 0.6045 (m-80)
REVERT: B   73 PHE cc_start: 0.8621 (t80) cc_final: 0.8404 (t80)
REVERT: B   80 LYS cc_start: 0.8485 (mtmm) cc_final: 0.8093 (mtmm)
REVERT: B   88 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7750 (mm-30)
REVERT: B  134 LEU cc_start: 0.8936 (mt) cc_final: 0.8375 (mt)
REVERT: B  173 HIS cc_start: 0.7815 (OUTLIER) cc_final: 0.7488 (m-70)
REVERT: B  180 MET cc_start: 0.8681 (mpp) cc_final: 0.8113 (mpp)
REVERT: B  198 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9081 (mp)
REVERT: B  209 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7456 (p0)
REVERT: B  234 LEU cc_start: 0.9299 (mm) cc_final: 0.9076 (mm)
REVERT: B  276 TYR cc_start: 0.8805 (m-80) cc_final: 0.8579 (m-80)
REVERT: B  334 GLU cc_start: 0.8641 (tp30) cc_final: 0.8422 (tp30)
REVERT: B  345 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7606 (mm-30)
REVERT: B  357 LYS cc_start: 0.8946 (mtmm) cc_final: 0.8699 (mtmt)
REVERT: B  365 GLN cc_start: 0.8582 (tp40) cc_final: 0.8240 (tp40)
REVERT: B  368 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8379 (tm-30)
REVERT: A   38 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8866 (mm-40)
REVERT: A   80 LYS cc_start: 0.8317 (mtmm) cc_final: 0.7855 (mtmm)
REVERT: A   84 ASP cc_start: 0.7979 (m-30) cc_final: 0.7719 (m-30)
REVERT: A  257 LYS cc_start: 0.8839 (tppp) cc_final: 0.8492 (tppt)
REVERT: A  337 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9079 (mm)
REVERT: A  345 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8266 (mm-30)
REVERT: A  354 GLU cc_start: 0.8508 (tp30) cc_final: 0.7935 (tt0)
REVERT: A  357 LYS cc_start: 0.8543 (pttp) cc_final: 0.8003 (ptpp)
REVERT: A  360 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7912 (mt-10)
REVERT: A  368 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8072 (tm-30)
REVERT: C    3 ASP cc_start: 0.8603 (t0) cc_final: 0.8334 (t0)
REVERT: C   47 ILE cc_start: 0.9134 (mm) cc_final: 0.8909 (mp)
REVERT: C   64 HIS cc_start: 0.8588 (t-90) cc_final: 0.8315 (t-90)
REVERT: C   65 TYR cc_start: 0.6625 (m-80) cc_final: 0.6201 (m-80)
REVERT: C   80 LYS cc_start: 0.8501 (mtmm) cc_final: 0.7897 (mtmm)
REVERT: C   84 ASP cc_start: 0.8337 (m-30) cc_final: 0.8011 (m-30)
REVERT: C  198 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9156 (mp)
REVERT: C  252 ARG cc_start: 0.8325 (mmt90) cc_final: 0.8035 (mmt90)
REVERT: C  281 ARG cc_start: 0.8573 (tpp-160) cc_final: 0.8228 (tpp80)
REVERT: C  356 ARG cc_start: 0.7540 (mmt-90) cc_final: 0.7050 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8740 (mtmm) cc_final: 0.8506 (mtmm)
REVERT: C  365 GLN cc_start: 0.8743 (tp40) cc_final: 0.8264 (tp-100)
REVERT: C  368 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8108 (tm-30)
REVERT: C  383 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8351 (tm-30)
  outliers start: 39
  outliers final: 29
  residues processed: 338
  average time/residue: 0.1216
  time to fit residues: 54.9738
Evaluate side-chains
  341 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 307
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  209 ASP
Chi-restraints excluded: chain B residue  255 LYS
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   30 ASN
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  379 SER
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue   31 HIS
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  319 VAL
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 115 optimal weight:    5.9990
   chunk 110 optimal weight:    0.9980
   chunk 85 optimal weight:    9.9990
   chunk 44 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 30 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 83 optimal weight:    0.0670
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.182613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.156114 restraints weight = 19186.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.4126 rms_B_bonded: 3.88
r_work (final): 0.4126
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4126
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4126 r_free = 0.4126    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4127 r_free = 0.4127    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4127
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          1.3447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.193  10450  Z= 0.468
  Angle     :  2.094  71.604  14404  Z= 0.917
  Chirality :  0.221   4.275   1722
  Planarity :  0.007   0.101   1632
  Dihedral  : 22.047 173.393   1932
  Min Nonbonded Distance : 1.736

Molprobity Statistics.
  All-atom Clashscore : 39.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 32.21 %
    Favored  : 64.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.25), residues: 1125
  helix:  0.24 (0.19), residues: 750
  sheet: -1.87 (0.55), residues: 72
  loop : -0.36 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG A 382 
 TYR   0.027   0.002   TYR A  65 
 PHE   0.027   0.002   PHE B 184 
 TRP   0.009   0.001   TRP C 174 
 HIS   0.005   0.001   HIS B 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00854 (10450)
  covalent geometry    : angle       2.09420 (14404)
  hydrogen bonds       : bond        0.42166 (  651)
  hydrogen bonds       : angle       5.56183 ( 1719)

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  360 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 327
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLU cc_start: 0.7233 (mt-10) cc_final: 0.7003 (mt-10)
REVERT: B   65 TYR cc_start: 0.6626 (m-80) cc_final: 0.6064 (m-80)
REVERT: B   80 LYS cc_start: 0.8440 (mtmm) cc_final: 0.8051 (mtmm)
REVERT: B   88 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7624 (mm-30)
REVERT: B  134 LEU cc_start: 0.8806 (mt) cc_final: 0.8273 (mt)
REVERT: B  173 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7523 (m-70)
REVERT: B  180 MET cc_start: 0.8780 (mpp) cc_final: 0.8147 (mpp)
REVERT: B  198 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9119 (mp)
REVERT: B  234 LEU cc_start: 0.9306 (mm) cc_final: 0.9101 (mm)
REVERT: B  345 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7537 (mm-30)
REVERT: B  357 LYS cc_start: 0.8829 (mtmm) cc_final: 0.8622 (mtmt)
REVERT: B  365 GLN cc_start: 0.8494 (tp40) cc_final: 0.8135 (tp40)
REVERT: B  368 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: B  382 ARG cc_start: 0.8635 (mmp80) cc_final: 0.8433 (mmp80)
REVERT: A   38 GLN cc_start: 0.9213 (mm-40) cc_final: 0.8879 (mm-40)
REVERT: A   80 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7803 (mtmm)
REVERT: A   84 ASP cc_start: 0.7926 (m-30) cc_final: 0.7697 (m-30)
REVERT: A  252 ARG cc_start: 0.7944 (mmt90) cc_final: 0.7709 (mmt90)
REVERT: A  337 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9110 (mm)
REVERT: A  345 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8390 (mm-30)
REVERT: A  354 GLU cc_start: 0.8402 (tp30) cc_final: 0.7900 (tt0)
REVERT: A  356 ARG cc_start: 0.7870 (mmt-90) cc_final: 0.7284 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8544 (pttp) cc_final: 0.7934 (ptpp)
REVERT: A  360 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7917 (mt-10)
REVERT: A  368 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8033 (tm-30)
REVERT: C    3 ASP cc_start: 0.8533 (t0) cc_final: 0.8275 (t0)
REVERT: C   33 VAL cc_start: 0.8847 (m) cc_final: 0.8594 (m)
REVERT: C   65 TYR cc_start: 0.6559 (m-80) cc_final: 0.6127 (m-80)
REVERT: C   80 LYS cc_start: 0.8497 (mtmm) cc_final: 0.7925 (mtmm)
REVERT: C   84 ASP cc_start: 0.8320 (m-30) cc_final: 0.8011 (m-30)
REVERT: C  356 ARG cc_start: 0.7537 (mmt-90) cc_final: 0.7088 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8663 (mtmm) cc_final: 0.8304 (mtmm)
REVERT: C  365 GLN cc_start: 0.8692 (tp40) cc_final: 0.8208 (tp-100)
REVERT: C  368 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8052 (tm-30)
REVERT: C  383 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8285 (tm-30)
  outliers start: 33
  outliers final: 24
  residues processed: 341
  average time/residue: 0.1271
  time to fit residues: 58.2153
Evaluate side-chains
  340 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 313
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  275 GLU
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   30 ASN
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  188 ARG
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  379 SER
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue   31 HIS
Chi-restraints excluded: chain C residue  216 SER
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 49 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0370
   chunk 103 optimal weight:    6.9990
   chunk 113 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 86 optimal weight:   10.0000
   chunk 66 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.9062

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

Flipped N/Q/H residues before XYZ refinement:
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 298 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.181137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.154224 restraints weight = 19100.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.4086 rms_B_bonded: 3.82
r_work (final): 0.4086
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4086
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4086 r_free = 0.4086    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4086 r_free = 0.4086    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4086
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7140
moved from start:          1.3633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.192  10450  Z= 0.461
  Angle     :  2.090  71.717  14404  Z= 0.909
  Chirality :  0.216   4.264   1722
  Planarity :  0.006   0.109   1632
  Dihedral  : 22.326 173.765   1932
  Min Nonbonded Distance : 1.735

Molprobity Statistics.
  All-atom Clashscore : 37.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 33.13 %
    Favored  : 63.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.25), residues: 1125
  helix:  0.23 (0.18), residues: 750
  sheet: -1.99 (0.55), residues: 72
  loop : -0.33 (0.40), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 327 
 TYR   0.027   0.002   TYR A  65 
 PHE   0.031   0.003   PHE B  73 
 TRP   0.011   0.001   TRP C 174 
 HIS   0.005   0.001   HIS C 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00855 (10450)
  covalent geometry    : angle       2.08951 (14404)
  hydrogen bonds       : bond        0.41863 (  651)
  hydrogen bonds       : angle       5.45677 ( 1719)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2737.24 seconds
wall clock time: 48 minutes 2.89 seconds (2882.89 seconds total)