Starting phenix.real_space_refine
on Thu May  1 01:37:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fvd_50803/05_2025/9fvd_50803.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fvd_50803/05_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_50803/05_2025/9fvd_50803.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fvd_50803/05_2025/9fvd_50803.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fvd_50803/05_2025/9fvd_50803.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fvd_50803/05_2025/9fvd_50803.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 7.88, per 1000 atoms: 0.78
  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: 4.01
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 6.06
  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: 3.87

  Time building geometry restraints manager: 4.47 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:             8.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     34.960
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.970
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.012   0.002   TRP A 174 
 HIS   0.004   0.001   HIS C  64 
 PHE   0.013   0.001   PHE B 195 
 TYR   0.025   0.002   TYR A 211 
 ARG   0.005   0.001   ARG A  20 

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

*********************** 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  : 0.967 
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: 0.2971
  time to fit residues: 146.5019
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  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   chunk 91 optimal weight:    0.5980
   chunk 35 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.165759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.141909 restraints weight = 19756.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 3.87
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3928
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3928 r_free = 0.3928    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3917 r_free = 0.3917    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
r_final: 0.3917
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.7287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.019   0.293  10450  Z= 1.117
  Angle     :  3.857  75.764  14404  Z= 1.704
  Chirality :  0.332   4.696   1722
  Planarity :  0.011   0.138   1632
  Dihedral  : 20.408 168.985   1932
  Min Nonbonded Distance : 1.627

Molprobity Statistics.
  All-atom Clashscore : 44.92
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.47 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 16.21 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.25), residues: 1125
  helix:  1.16 (0.19), residues: 717
  sheet: -1.97 (0.85), residues: 30
  loop : -1.15 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 174 
 HIS   0.013   0.001   HIS A 293 
 PHE   0.025   0.002   PHE C 184 
 TYR   0.037   0.003   TYR B 211 
 ARG   0.023   0.002   ARG C 157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.60111 (  651)
  hydrogen bonds       : angle       5.57941 ( 1719)
  covalent geometry    : bond        0.01896 (10450)
  covalent geometry    : angle       3.85733 (14404)

*********************** 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
  409 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 375
  time to evaluate  : 1.013 
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: 0.6401 (m-80) cc_final: 0.6018 (m-80)
REVERT: B   80 LYS cc_start: 0.8480 (mtmm) cc_final: 0.8175 (mtmm)
REVERT: B   88 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8047 (mm-30)
REVERT: B  153 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8265 (mm-30)
REVERT: B  198 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.9017 (mp)
REVERT: B  212 ASP cc_start: 0.8550 (m-30) cc_final: 0.8199 (m-30)
REVERT: B  345 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8262 (mm-30)
REVERT: B  357 LYS cc_start: 0.8788 (mtmm) cc_final: 0.8208 (mtmt)
REVERT: B  380 GLN cc_start: 0.8599 (tp40) cc_final: 0.8389 (tp-100)
REVERT: B  383 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8193 (tm-30)
REVERT: A   47 ILE cc_start: 0.9158 (mm) cc_final: 0.8869 (mp)
REVERT: A   71 ASP cc_start: 0.8202 (t0) cc_final: 0.7916 (t0)
REVERT: A   80 LYS cc_start: 0.8399 (mtmm) cc_final: 0.7948 (mtmm)
REVERT: A   81 TYR cc_start: 0.8497 (t80) cc_final: 0.8097 (t80)
REVERT: A   84 ASP cc_start: 0.8014 (m-30) cc_final: 0.7724 (m-30)
REVERT: A  198 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9003 (mp)
REVERT: A  252 ARG cc_start: 0.8189 (mmt90) cc_final: 0.7966 (mmt90)
REVERT: A  308 THR cc_start: 0.7531 (m) cc_final: 0.7070 (m)
REVERT: A  322 GLN cc_start: 0.9131 (pm20) cc_final: 0.8855 (pm20)
REVERT: A  323 TYR cc_start: 0.8904 (m-80) cc_final: 0.8476 (m-80)
REVERT: A  324 GLN cc_start: 0.8351 (mt0) cc_final: 0.8082 (mm-40)
REVERT: A  325 GLN cc_start: 0.8557 (mp10) cc_final: 0.8294 (mp10)
REVERT: A  342 GLU cc_start: 0.8223 (pp20) cc_final: 0.7848 (pp20)
REVERT: A  345 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8195 (mm-30)
REVERT: A  356 ARG cc_start: 0.7556 (mmt-90) cc_final: 0.7227 (mmt-90)
REVERT: A  368 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8666 (tm-30)
REVERT: A  380 GLN cc_start: 0.8643 (tp-100) cc_final: 0.8400 (tp-100)
REVERT: A  383 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7856 (tm-30)
REVERT: C   32 GLN cc_start: 0.8780 (tp-100) cc_final: 0.8535 (tp-100)
REVERT: C   65 TYR cc_start: 0.6406 (m-10) cc_final: 0.6191 (m-80)
REVERT: C  180 MET cc_start: 0.8659 (mpp) cc_final: 0.8390 (mpp)
REVERT: C  198 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9067 (mp)
REVERT: C  252 ARG cc_start: 0.8209 (mmt90) cc_final: 0.7897 (mmt90)
REVERT: C  275 GLU cc_start: 0.8357 (mp0) cc_final: 0.8132 (mp0)
REVERT: C  325 GLN cc_start: 0.8734 (mp10) cc_final: 0.8466 (mp10)
REVERT: C  345 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8246 (mm-30)
REVERT: C  356 ARG cc_start: 0.7526 (mmt-90) cc_final: 0.6970 (mmt-90)
REVERT: C  357 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8405 (mtmm)
REVERT: C  380 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8413 (tp40)
REVERT: C  382 ARG cc_start: 0.8416 (mmp80) cc_final: 0.8000 (mmp-170)
REVERT: C  383 GLU cc_start: 0.8360 (tm-30) cc_final: 0.8078 (tm-30)
  outliers start: 34
  outliers final: 16
  residues processed: 395
  average time/residue: 0.2781
  time to fit residues: 143.4350
Evaluate side-chains
  357 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 337
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
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  247 LEU
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  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 32 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 104 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.9990

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A  32 GLN
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  21 ASN
C  64 HIS
** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.169951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.145117 restraints weight = 19503.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 3.88
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3990
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3990 r_free = 0.3990    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3986 r_free = 0.3986    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3986
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.9098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.202  10450  Z= 0.703
  Angle     :  2.681  71.290  14404  Z= 1.207
  Chirality :  0.317   4.680   1722
  Planarity :  0.008   0.086   1632
  Dihedral  : 20.806 171.892   1932
  Min Nonbonded Distance : 1.766

Molprobity Statistics.
  All-atom Clashscore : 45.46
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.53 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 17.53 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.25), residues: 1125
  helix:  1.22 (0.19), residues: 720
  sheet: -2.27 (0.89), residues: 30
  loop : -1.24 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 174 
 HIS   0.006   0.001   HIS A 331 
 PHE   0.029   0.002   PHE C 184 
 TYR   0.034   0.002   TYR C 323 
 ARG   0.016   0.001   ARG A 327 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.55992 (  651)
  hydrogen bonds       : angle       5.10985 ( 1719)
  covalent geometry    : bond        0.01214 (10450)
  covalent geometry    : angle       2.68107 (14404)

*********************** 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
  447 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 390
  time to evaluate  : 1.006 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.6540 (m-80) cc_final: 0.6228 (m-80)
REVERT: B   88 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7877 (mm-30)
REVERT: B  133 PHE cc_start: 0.8712 (t80) cc_final: 0.8477 (t80)
REVERT: B  134 LEU cc_start: 0.9301 (mt) cc_final: 0.8840 (mt)
REVERT: B  148 ASP cc_start: 0.6809 (p0) cc_final: 0.6383 (p0)
REVERT: B  152 ILE cc_start: 0.8744 (pt) cc_final: 0.8539 (pt)
REVERT: B  153 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7674 (mm-30)
REVERT: B  180 MET cc_start: 0.8767 (mpp) cc_final: 0.8525 (mpp)
REVERT: B  198 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9020 (mp)
REVERT: B  252 ARG cc_start: 0.8154 (mmt90) cc_final: 0.7880 (mmt90)
REVERT: B  259 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7729 (mm-30)
REVERT: B  308 THR cc_start: 0.7638 (m) cc_final: 0.7405 (m)
REVERT: B  319 VAL cc_start: 0.3463 (OUTLIER) cc_final: 0.3228 (t)
REVERT: B  323 TYR cc_start: 0.8603 (m-80) cc_final: 0.8155 (m-80)
REVERT: B  345 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8309 (mm-30)
REVERT: B  356 ARG cc_start: 0.7738 (mmt-90) cc_final: 0.7365 (mmt-90)
REVERT: B  380 GLN cc_start: 0.8800 (tp40) cc_final: 0.8561 (tp40)
REVERT: B  383 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8247 (tm-30)
REVERT: A    2 MET cc_start: 0.8492 (ppp) cc_final: 0.8221 (ppp)
REVERT: A   44 ASN cc_start: 0.9094 (p0) cc_final: 0.8638 (p0)
REVERT: A   65 TYR cc_start: 0.5635 (m-80) cc_final: 0.5173 (m-80)
REVERT: A   80 LYS cc_start: 0.8344 (mtmm) cc_final: 0.7873 (mtmm)
REVERT: A   81 TYR cc_start: 0.8551 (t80) cc_final: 0.8332 (t80)
REVERT: A   84 ASP cc_start: 0.7972 (m-30) cc_final: 0.7693 (m-30)
REVERT: A  198 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9073 (mp)
REVERT: A  200 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7475 (mm-40)
REVERT: A  252 ARG cc_start: 0.8208 (mmt90) cc_final: 0.7961 (mmt90)
REVERT: A  288 ILE cc_start: 0.8556 (tp) cc_final: 0.8147 (tp)
REVERT: A  295 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7711 (mp)
REVERT: A  308 THR cc_start: 0.8122 (m) cc_final: 0.7266 (m)
REVERT: A  324 GLN cc_start: 0.8598 (mt0) cc_final: 0.8246 (mm-40)
REVERT: A  337 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8889 (mm)
REVERT: A  345 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8193 (mm-30)
REVERT: A  354 GLU cc_start: 0.8749 (tp30) cc_final: 0.8468 (pt0)
REVERT: A  356 ARG cc_start: 0.7537 (mmt-90) cc_final: 0.7024 (mmt-90)
REVERT: A  361 GLN cc_start: 0.8765 (tp40) cc_final: 0.8524 (tm-30)
REVERT: A  380 GLN cc_start: 0.8531 (tp-100) cc_final: 0.8271 (tp40)
REVERT: A  383 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8085 (tm-30)
REVERT: A  385 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8516 (mt)
REVERT: C   32 GLN cc_start: 0.8808 (tp-100) cc_final: 0.8528 (tp-100)
REVERT: C   37 ASN cc_start: 0.9139 (m-40) cc_final: 0.8917 (m-40)
REVERT: C   64 HIS cc_start: 0.8783 (t-90) cc_final: 0.8524 (t-90)
REVERT: C   80 LYS cc_start: 0.8461 (mtmm) cc_final: 0.7940 (mtmm)
REVERT: C   87 TYR cc_start: 0.8740 (m-80) cc_final: 0.8527 (m-80)
REVERT: C  180 MET cc_start: 0.8746 (mpp) cc_final: 0.8500 (mpp)
REVERT: C  198 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9010 (mp)
REVERT: C  234 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8976 (mm)
REVERT: C  247 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8726 (tp)
REVERT: C  252 ARG cc_start: 0.8131 (mmt90) cc_final: 0.7829 (mmt90)
REVERT: C  308 THR cc_start: 0.8095 (m) cc_final: 0.7869 (m)
REVERT: C  345 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8249 (mm-30)
REVERT: C  356 ARG cc_start: 0.7540 (mmt-90) cc_final: 0.6972 (mmt-90)
REVERT: C  380 GLN cc_start: 0.8717 (tp40) cc_final: 0.8464 (tp40)
REVERT: C  383 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8079 (tm-30)
  outliers start: 57
  outliers final: 23
  residues processed: 421
  average time/residue: 0.2585
  time to fit residues: 143.5603
Evaluate side-chains
  385 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 353
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
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  232 THR
Chi-restraints excluded: chain B residue  268 SER
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  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 A residue  377 VAL
Chi-restraints excluded: chain A residue  382 ARG
Chi-restraints excluded: chain A residue  385 LEU
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  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  319 VAL
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 11 optimal weight:    0.2980
   chunk 110 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 94 optimal weight:    0.8980
   chunk 114 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0060
   chunk 39 optimal weight:   20.0000
   chunk 41 optimal weight:    4.9990
   overall best weight:    1.0198

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

Flipped N/Q/H residues before XYZ refinement:
B 289 ASN
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 GLN
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 344 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 = 0.4282 r_free = 0.4282 target = 0.172363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.146606 restraints weight = 19441.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 3.98
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3987
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3987 r_free = 0.3987    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3983 r_free = 0.3983    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3983
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.9941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.206  10450  Z= 0.593
  Angle     :  2.376  70.328  14404  Z= 1.056
  Chirality :  0.300   4.622   1722
  Planarity :  0.007   0.087   1632
  Dihedral  : 21.982 171.128   1932
  Min Nonbonded Distance : 1.757

Molprobity Statistics.
  All-atom Clashscore : 41.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 22.43 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.25), residues: 1125
  helix:  1.24 (0.19), residues: 720
  sheet: -2.34 (0.89), residues: 30
  loop : -1.11 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 174 
 HIS   0.007   0.001   HIS B 331 
 PHE   0.017   0.002   PHE B  27 
 TYR   0.033   0.002   TYR A 323 
 ARG   0.010   0.001   ARG A 327 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.49881 (  651)
  hydrogen bonds       : angle       5.05840 ( 1719)
  covalent geometry    : bond        0.01039 (10450)
  covalent geometry    : angle       2.37633 (14404)

*********************** 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
  425 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 371
  time to evaluate  : 1.237 
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: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.6774 (m-80) cc_final: 0.6366 (m-80)
REVERT: B   80 LYS cc_start: 0.8466 (mtmm) cc_final: 0.8037 (mtmm)
REVERT: B   83 ARG cc_start: 0.8118 (mmp-170) cc_final: 0.7915 (mmp-170)
REVERT: B   88 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7780 (mm-30)
REVERT: B  148 ASP cc_start: 0.6608 (p0) cc_final: 0.5992 (p0)
REVERT: B  180 MET cc_start: 0.8874 (mpp) cc_final: 0.8600 (mpp)
REVERT: B  184 PHE cc_start: 0.9090 (t80) cc_final: 0.8881 (t80)
REVERT: B  198 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9080 (mp)
REVERT: B  234 LEU cc_start: 0.9437 (mt) cc_final: 0.9132 (mt)
REVERT: B  331 HIS cc_start: 0.6844 (t70) cc_final: 0.6434 (t70)
REVERT: B  345 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8436 (mm-30)
REVERT: B  356 ARG cc_start: 0.7876 (mmt-90) cc_final: 0.7352 (mmt-90)
REVERT: B  357 LYS cc_start: 0.9018 (mtmm) cc_final: 0.8398 (mtmm)
REVERT: B  365 GLN cc_start: 0.8813 (tp40) cc_final: 0.8470 (tp-100)
REVERT: B  380 GLN cc_start: 0.8858 (tp40) cc_final: 0.8596 (tp-100)
REVERT: B  383 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8259 (tm-30)
REVERT: A   44 ASN cc_start: 0.9107 (p0) cc_final: 0.8601 (p0)
REVERT: A   47 ILE cc_start: 0.9088 (mm) cc_final: 0.8824 (mp)
REVERT: A   65 TYR cc_start: 0.6055 (m-80) cc_final: 0.5561 (m-80)
REVERT: A   80 LYS cc_start: 0.8343 (mtmm) cc_final: 0.7893 (mtmm)
REVERT: A   84 ASP cc_start: 0.8034 (m-30) cc_final: 0.7734 (m-30)
REVERT: A  198 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9101 (mp)
REVERT: A  200 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7546 (mm-40)
REVERT: A  337 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8988 (mm)
REVERT: A  345 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8236 (mm-30)
REVERT: A  354 GLU cc_start: 0.8398 (tp30) cc_final: 0.7917 (tt0)
REVERT: A  356 ARG cc_start: 0.7620 (mmt-90) cc_final: 0.7122 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8667 (pttp) cc_final: 0.8165 (ptpp)
REVERT: A  361 GLN cc_start: 0.8750 (tp40) cc_final: 0.8515 (tm-30)
REVERT: A  380 GLN cc_start: 0.8595 (tp-100) cc_final: 0.8308 (tp-100)
REVERT: A  383 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8147 (tm-30)
REVERT: C   32 GLN cc_start: 0.8810 (tp-100) cc_final: 0.8514 (tp-100)
REVERT: C   47 ILE cc_start: 0.9190 (mm) cc_final: 0.8835 (mp)
REVERT: C   64 HIS cc_start: 0.8651 (t-90) cc_final: 0.8221 (t-90)
REVERT: C   65 TYR cc_start: 0.6499 (m-80) cc_final: 0.6120 (m-80)
REVERT: C   80 LYS cc_start: 0.8461 (mtmm) cc_final: 0.8031 (mtmm)
REVERT: C   87 TYR cc_start: 0.8736 (m-80) cc_final: 0.8525 (m-80)
REVERT: C  145 VAL cc_start: 0.2821 (OUTLIER) cc_final: 0.2522 (t)
REVERT: C  165 GLN cc_start: 0.5814 (OUTLIER) cc_final: 0.4980 (mt0)
REVERT: C  173 HIS cc_start: 0.8081 (t-90) cc_final: 0.7791 (t-90)
REVERT: C  184 PHE cc_start: 0.9036 (t80) cc_final: 0.8770 (t80)
REVERT: C  198 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9107 (mp)
REVERT: C  234 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9140 (mm)
REVERT: C  247 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8771 (tp)
REVERT: C  252 ARG cc_start: 0.8295 (mmt90) cc_final: 0.7824 (mmt90)
REVERT: C  259 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8481 (mm-30)
REVERT: C  345 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8303 (mm-30)
REVERT: C  356 ARG cc_start: 0.7473 (mmt-90) cc_final: 0.6705 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8813 (mtmm) cc_final: 0.8303 (mtmm)
REVERT: C  365 GLN cc_start: 0.8866 (tp40) cc_final: 0.8531 (tp-100)
REVERT: C  383 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8130 (tm-30)
  outliers start: 54
  outliers final: 22
  residues processed: 397
  average time/residue: 0.3299
  time to fit residues: 172.2479
Evaluate side-chains
  376 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 346
  time to evaluate  : 2.006 
-------------------------------------------------------------------------------
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  268 SER
Chi-restraints excluded: chain B residue  313 THR
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  144 LEU
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  197 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  209 ASP
Chi-restraints excluded: chain C residue  212 ASP
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
Chi-restraints excluded: chain C residue  323 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 11 optimal weight:    7.9990
   chunk 59 optimal weight:    0.8980
   chunk 71 optimal weight:    6.9990
   chunk 116 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 110 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 82 optimal weight:    9.9990
   chunk 6 optimal weight:   10.0000
   overall best weight:    3.3788

-------------------------------------------------------------------------------
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 163 GLN
B 380 GLN
A 293 HIS
** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 109 HIS
C 172 ASN
** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 338 GLN
** C 344 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 = 0.4158 r_free = 0.4158 target = 0.159957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.135589 restraints weight = 19723.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.3843 rms_B_bonded: 3.72
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3854
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3854 r_free = 0.3854    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3853 r_free = 0.3853    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3853
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          1.0101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.202  10450  Z= 0.579
  Angle     :  2.288  70.711  14404  Z= 1.029
  Chirality :  0.288   4.669   1722
  Planarity :  0.008   0.136   1632
  Dihedral  : 22.521 172.397   1932
  Min Nonbonded Distance : 1.756

Molprobity Statistics.
  All-atom Clashscore : 45.65
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.51 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 22.83 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.25), residues: 1125
  helix:  0.95 (0.19), residues: 723
  sheet: -0.90 (0.60), residues: 72
  loop : -1.07 (0.36), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 174 
 HIS   0.008   0.001   HIS A 293 
 PHE   0.034   0.003   PHE A 184 
 TYR   0.025   0.002   TYR B 211 
 ARG   0.012   0.001   ARG B 157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.47654 (  651)
  hydrogen bonds       : angle       5.21422 ( 1719)
  covalent geometry    : bond        0.01079 (10450)
  covalent geometry    : angle       2.28783 (14404)

*********************** 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
  431 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 369
  time to evaluate  : 1.111 
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: 0.6684 (m-80) cc_final: 0.6143 (m-80)
REVERT: B   88 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7952 (mm-30)
REVERT: B  173 HIS cc_start: 0.8003 (OUTLIER) cc_final: 0.7498 (m-70)
REVERT: B  198 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9121 (mp)
REVERT: B  211 TYR cc_start: 0.7592 (m-80) cc_final: 0.7108 (m-10)
REVERT: B  276 TYR cc_start: 0.9003 (m-80) cc_final: 0.8798 (m-80)
REVERT: B  331 HIS cc_start: 0.7385 (t70) cc_final: 0.7089 (t70)
REVERT: B  345 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8462 (mm-30)
REVERT: B  380 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8514 (tp-100)
REVERT: B  383 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: A   64 HIS cc_start: 0.8727 (t-90) cc_final: 0.8390 (t70)
REVERT: A   80 LYS cc_start: 0.8345 (mtmm) cc_final: 0.7853 (mtmm)
REVERT: A   84 ASP cc_start: 0.8072 (m-30) cc_final: 0.7812 (m-30)
REVERT: A  163 GLN cc_start: 0.8364 (pt0) cc_final: 0.8069 (pp30)
REVERT: A  164 GLU cc_start: 0.6664 (tm-30) cc_final: 0.6453 (tt0)
REVERT: A  194 LYS cc_start: 0.8939 (mttm) cc_final: 0.8526 (mttt)
REVERT: A  198 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9116 (mp)
REVERT: A  252 ARG cc_start: 0.8368 (mmt90) cc_final: 0.8082 (mmt90)
REVERT: A  259 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8300 (mm-30)
REVERT: A  337 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8981 (mm)
REVERT: A  345 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8267 (mm-30)
REVERT: A  354 GLU cc_start: 0.8552 (tp30) cc_final: 0.7820 (tt0)
REVERT: A  356 ARG cc_start: 0.7802 (mmt-90) cc_final: 0.7371 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8681 (pttp) cc_final: 0.8269 (ptpp)
REVERT: A  380 GLN cc_start: 0.8689 (tp-100) cc_final: 0.8194 (tp-100)
REVERT: A  383 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8075 (tm-30)
REVERT: C    3 ASP cc_start: 0.8575 (t0) cc_final: 0.8357 (t0)
REVERT: C   65 TYR cc_start: 0.6633 (m-80) cc_final: 0.6401 (m-80)
REVERT: C   80 LYS cc_start: 0.8652 (mtmm) cc_final: 0.7951 (mtmm)
REVERT: C   84 ASP cc_start: 0.8324 (m-30) cc_final: 0.8049 (m-30)
REVERT: C   87 TYR cc_start: 0.8849 (m-80) cc_final: 0.8530 (m-80)
REVERT: C  165 GLN cc_start: 0.5729 (OUTLIER) cc_final: 0.5317 (mt0)
REVERT: C  180 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8515 (mpp)
REVERT: C  198 ILE cc_start: 0.9436 (OUTLIER) cc_final: 0.9145 (mp)
REVERT: C  234 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9172 (mm)
REVERT: C  252 ARG cc_start: 0.8371 (mmt90) cc_final: 0.8012 (mmt90)
REVERT: C  255 LYS cc_start: 0.3418 (mmtt) cc_final: 0.3207 (tptt)
REVERT: C  281 ARG cc_start: 0.8755 (tpp-160) cc_final: 0.8402 (tpp80)
REVERT: C  324 GLN cc_start: 0.7399 (mm-40) cc_final: 0.7179 (mm-40)
REVERT: C  340 ARG cc_start: 0.8721 (mmm-85) cc_final: 0.8331 (mmm160)
REVERT: C  356 ARG cc_start: 0.7713 (mmt-90) cc_final: 0.7169 (mmt-90)
REVERT: C  365 GLN cc_start: 0.8934 (tp40) cc_final: 0.8536 (tp-100)
REVERT: C  383 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8071 (tm-30)
  outliers start: 62
  outliers final: 38
  residues processed: 399
  average time/residue: 0.2695
  time to fit residues: 141.3112
Evaluate side-chains
  388 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 342
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   48 ASP
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  186 ILE
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   30 ASN
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  197 LEU
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  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  104 ILE
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  165 GLN
Chi-restraints excluded: chain C residue  180 MET
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  209 ASP
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  253 THR
Chi-restraints excluded: chain C residue  257 LYS
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  313 THR
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  374 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 23 optimal weight:    0.0570
   chunk 70 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 90 optimal weight:    6.9990
   chunk 34 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 76 optimal weight:    9.9990
   overall best weight:    1.3302

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

Flipped N/Q/H residues before XYZ refinement:
B 324 GLN
** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 380 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.170276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.145328 restraints weight = 19923.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3988 rms_B_bonded: 3.85
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3989
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3989 r_free = 0.3989    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3988 r_free = 0.3988    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3988
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          1.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.200  10450  Z= 0.495
  Angle     :  2.107  71.084  14404  Z= 0.942
  Chirality :  0.268   4.615   1722
  Planarity :  0.007   0.091   1632
  Dihedral  : 22.172 174.026   1932
  Min Nonbonded Distance : 1.753

Molprobity Statistics.
  All-atom Clashscore : 40.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 26.40 %
    Favored  : 67.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.26), residues: 1125
  helix:  0.83 (0.19), residues: 738
  sheet: -1.01 (0.57), residues: 72
  loop : -0.61 (0.39), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 174 
 HIS   0.006   0.001   HIS A 331 
 PHE   0.030   0.002   PHE A 184 
 TYR   0.021   0.002   TYR B 211 
 ARG   0.022   0.001   ARG B 157 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.46516 (  651)
  hydrogen bonds       : angle       5.22860 ( 1719)
  covalent geometry    : bond        0.00901 (10450)
  covalent geometry    : angle       2.10710 (14404)

*********************** 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
  428 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 369
  time to evaluate  : 1.141 
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   47 ILE cc_start: 0.9139 (mm) cc_final: 0.8858 (mp)
REVERT: B   65 TYR cc_start: 0.6590 (m-80) cc_final: 0.6088 (m-80)
REVERT: B   80 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8083 (mtmm)
REVERT: B  110 TYR cc_start: 0.7456 (m-80) cc_final: 0.7127 (m-10)
REVERT: B  149 ARG cc_start: 0.7892 (mmm-85) cc_final: 0.7662 (mmm-85)
REVERT: B  198 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9073 (mp)
REVERT: B  204 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7978 (tt)
REVERT: B  211 TYR cc_start: 0.7531 (m-80) cc_final: 0.7067 (m-80)
REVERT: B  257 LYS cc_start: 0.8913 (tppp) cc_final: 0.8684 (mmtp)
REVERT: B  259 GLU cc_start: 0.8256 (mm-30) cc_final: 0.8012 (mm-30)
REVERT: B  276 TYR cc_start: 0.8929 (m-80) cc_final: 0.8694 (m-80)
REVERT: B  281 ARG cc_start: 0.8364 (tpp80) cc_final: 0.7933 (tpp-160)
REVERT: B  331 HIS cc_start: 0.7152 (t70) cc_final: 0.6935 (t70)
REVERT: B  345 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8360 (mm-30)
REVERT: B  357 LYS cc_start: 0.8896 (mtmm) cc_final: 0.8652 (mtmm)
REVERT: B  383 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: A   64 HIS cc_start: 0.8518 (t-90) cc_final: 0.8126 (t70)
REVERT: A   80 LYS cc_start: 0.8421 (mtmm) cc_final: 0.7918 (mtmm)
REVERT: A   83 ARG cc_start: 0.8166 (mmp-170) cc_final: 0.7963 (mmp-170)
REVERT: A   84 ASP cc_start: 0.7963 (m-30) cc_final: 0.7708 (m-30)
REVERT: A  194 LYS cc_start: 0.8950 (mttm) cc_final: 0.8563 (mttt)
REVERT: A  198 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9069 (mp)
REVERT: A  200 GLN cc_start: 0.7689 (mm-40) cc_final: 0.7436 (mm-40)
REVERT: A  252 ARG cc_start: 0.8160 (mmt90) cc_final: 0.7480 (mmt90)
REVERT: A  257 LYS cc_start: 0.9067 (tppp) cc_final: 0.8596 (tppp)
REVERT: A  259 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8371 (mm-30)
REVERT: A  337 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9064 (mm)
REVERT: A  345 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8314 (mm-30)
REVERT: A  354 GLU cc_start: 0.8517 (tp30) cc_final: 0.7757 (tt0)
REVERT: A  356 ARG cc_start: 0.7777 (mmt-90) cc_final: 0.7410 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8591 (pttp) cc_final: 0.8182 (ptpp)
REVERT: A  383 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8228 (tm-30)
REVERT: C   32 GLN cc_start: 0.8871 (tp-100) cc_final: 0.8556 (tp-100)
REVERT: C   37 ASN cc_start: 0.9161 (m-40) cc_final: 0.8939 (m-40)
REVERT: C   47 ILE cc_start: 0.9171 (mm) cc_final: 0.8822 (mp)
REVERT: C   64 HIS cc_start: 0.8650 (t-90) cc_final: 0.8271 (t-90)
REVERT: C   65 TYR cc_start: 0.6699 (m-80) cc_final: 0.6139 (m-80)
REVERT: C   80 LYS cc_start: 0.8556 (mtmm) cc_final: 0.7863 (mtmm)
REVERT: C   83 ARG cc_start: 0.8335 (mmp-170) cc_final: 0.8093 (mmp-170)
REVERT: C   84 ASP cc_start: 0.8248 (m-30) cc_final: 0.7969 (m-30)
REVERT: C   87 TYR cc_start: 0.8715 (m-80) cc_final: 0.7773 (m-80)
REVERT: C   88 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7418 (mm-30)
REVERT: C  180 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8519 (mpp)
REVERT: C  198 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9129 (mp)
REVERT: C  255 LYS cc_start: 0.3183 (mmtt) cc_final: 0.2664 (tptt)
REVERT: C  281 ARG cc_start: 0.8620 (tpp-160) cc_final: 0.8387 (tpp80)
REVERT: C  308 THR cc_start: 0.7298 (m) cc_final: 0.6821 (m)
REVERT: C  357 LYS cc_start: 0.9155 (mtpp) cc_final: 0.8870 (mtmm)
REVERT: C  365 GLN cc_start: 0.8874 (tp40) cc_final: 0.8485 (tp-100)
REVERT: C  382 ARG cc_start: 0.8346 (mmp80) cc_final: 0.8005 (mmp-170)
REVERT: C  383 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8102 (tm-30)
  outliers start: 59
  outliers final: 34
  residues processed: 395
  average time/residue: 0.3588
  time to fit residues: 189.4213
Evaluate side-chains
  385 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 345
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
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  104 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  204 LEU
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain A residue   30 ASN
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  144 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  296 TYR
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain C residue   23 LYS
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  154 LYS
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  197 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  313 THR
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 89 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 16 optimal weight:    7.9990
   chunk 22 optimal weight:    3.9990
   chunk 84 optimal weight:    5.9990
   chunk 71 optimal weight:    7.9990
   chunk 90 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B  74 ASN
B 380 GLN
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 380 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.172970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.147241 restraints weight = 19786.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.4025 rms_B_bonded: 3.81
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4025
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4025 r_free = 0.4025    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4024 r_free = 0.4024    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4024
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          1.1595

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= 0.479
  Angle     :  2.048  71.979  14404  Z= 0.918
  Chirality :  0.258   4.522   1722
  Planarity :  0.006   0.058   1632
  Dihedral  : 22.054 170.086   1932
  Min Nonbonded Distance : 1.750

Molprobity Statistics.
  All-atom Clashscore : 39.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 27.32 %
    Favored  : 66.16 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.25), residues: 1125
  helix:  0.63 (0.19), residues: 753
  sheet: -1.43 (0.52), residues: 72
  loop : -0.60 (0.39), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 174 
 HIS   0.007   0.001   HIS C 331 
 PHE   0.035   0.002   PHE A  73 
 TYR   0.023   0.002   TYR A 323 
 ARG   0.015   0.001   ARG A 382 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.42878 (  651)
  hydrogen bonds       : angle       5.24839 ( 1719)
  covalent geometry    : bond        0.00869 (10450)
  covalent geometry    : angle       2.04800 (14404)

*********************** 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
  425 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 361
  time to evaluate  : 1.028 
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: B   65 TYR cc_start: 0.6623 (m-80) cc_final: 0.6111 (m-80)
REVERT: B   80 LYS cc_start: 0.8358 (mtmm) cc_final: 0.8151 (mtmm)
REVERT: B  110 TYR cc_start: 0.7351 (m-80) cc_final: 0.6971 (m-10)
REVERT: B  118 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8544 (ptpp)
REVERT: B  173 HIS cc_start: 0.7891 (OUTLIER) cc_final: 0.7511 (m-70)
REVERT: B  198 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9098 (mp)
REVERT: B  211 TYR cc_start: 0.7523 (m-80) cc_final: 0.7189 (m-80)
REVERT: B  257 LYS cc_start: 0.9008 (tppp) cc_final: 0.8698 (mmtm)
REVERT: B  259 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7931 (mm-30)
REVERT: B  276 TYR cc_start: 0.8937 (m-80) cc_final: 0.8700 (m-80)
REVERT: B  345 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8401 (mm-30)
REVERT: B  357 LYS cc_start: 0.8943 (mtmm) cc_final: 0.8684 (mtmm)
REVERT: B  383 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8166 (tm-30)
REVERT: A   80 LYS cc_start: 0.8322 (mtmm) cc_final: 0.7853 (mtmm)
REVERT: A   84 ASP cc_start: 0.8062 (m-30) cc_final: 0.7787 (m-30)
REVERT: A  194 LYS cc_start: 0.8910 (mttm) cc_final: 0.8504 (mttm)
REVERT: A  198 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9112 (mp)
REVERT: A  200 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7528 (mm-40)
REVERT: A  252 ARG cc_start: 0.8180 (mmt90) cc_final: 0.7928 (mmt90)
REVERT: A  257 LYS cc_start: 0.9096 (tppp) cc_final: 0.8822 (mmmm)
REVERT: A  259 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8349 (mm-30)
REVERT: A  321 GLU cc_start: 0.8929 (mp0) cc_final: 0.8681 (mm-30)
REVERT: A  337 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9000 (mm)
REVERT: A  345 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8406 (mm-30)
REVERT: A  354 GLU cc_start: 0.8620 (tp30) cc_final: 0.7887 (tt0)
REVERT: A  355 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8445 (pm20)
REVERT: A  356 ARG cc_start: 0.7851 (mmt-90) cc_final: 0.7453 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8624 (pttp) cc_final: 0.8217 (ptpp)
REVERT: A  368 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8225 (tm-30)
REVERT: A  383 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8206 (tm-30)
REVERT: C   32 GLN cc_start: 0.8831 (tp-100) cc_final: 0.8518 (tp-100)
REVERT: C   47 ILE cc_start: 0.9185 (mm) cc_final: 0.8840 (mp)
REVERT: C   54 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7943 (mm-30)
REVERT: C   64 HIS cc_start: 0.8575 (t-90) cc_final: 0.8032 (t-90)
REVERT: C   65 TYR cc_start: 0.6846 (m-80) cc_final: 0.5977 (m-80)
REVERT: C   80 LYS cc_start: 0.8558 (mtmm) cc_final: 0.7900 (mtmm)
REVERT: C   83 ARG cc_start: 0.8411 (mmp-170) cc_final: 0.8185 (mmp-170)
REVERT: C   84 ASP cc_start: 0.8303 (m-30) cc_final: 0.8041 (m-30)
REVERT: C   87 TYR cc_start: 0.8705 (m-80) cc_final: 0.7699 (m-80)
REVERT: C  134 LEU cc_start: 0.9208 (mt) cc_final: 0.8677 (mt)
REVERT: C  180 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8502 (mpp)
REVERT: C  194 LYS cc_start: 0.8738 (mttm) cc_final: 0.8421 (mttm)
REVERT: C  198 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9140 (mp)
REVERT: C  255 LYS cc_start: 0.3338 (mmtt) cc_final: 0.2715 (tptt)
REVERT: C  308 THR cc_start: 0.7024 (m) cc_final: 0.6609 (m)
REVERT: C  324 GLN cc_start: 0.6701 (mm-40) cc_final: 0.6160 (mm-40)
REVERT: C  357 LYS cc_start: 0.9127 (mtpp) cc_final: 0.8835 (mtmm)
REVERT: C  365 GLN cc_start: 0.8908 (tp40) cc_final: 0.8567 (tp-100)
REVERT: C  383 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8149 (tm-30)
  outliers start: 64
  outliers final: 35
  residues processed: 392
  average time/residue: 0.2730
  time to fit residues: 142.1208
Evaluate side-chains
  386 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 344
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
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  267 LEU
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 B residue  378 LEU
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   61 CYS
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  189 SER
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  296 TYR
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  355 GLU
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  103 VAL
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  180 MET
Chi-restraints excluded: chain C residue  197 LEU
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  268 SER
Chi-restraints excluded: chain C residue  282 VAL
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  327 ARG
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 5 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 36 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0040
   chunk 73 optimal weight:    0.9990
   overall best weight:    1.1996

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

Flipped N/Q/H residues before XYZ refinement:
** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 298 GLN
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 ASN
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 380 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.175326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.149581 restraints weight = 19414.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 3.94
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4007 r_free = 0.4007    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4006 r_free = 0.4006    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4006
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          1.2147

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= 0.479
  Angle     :  2.033  70.922  14404  Z= 0.909
  Chirality :  0.233   4.510   1722
  Planarity :  0.006   0.062   1632
  Dihedral  : 21.733 167.897   1932
  Min Nonbonded Distance : 1.730

Molprobity Statistics.
  All-atom Clashscore : 40.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 28.44 %
    Favored  : 65.95 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.25), residues: 1125
  helix:  0.47 (0.19), residues: 759
  sheet: -1.48 (0.53), residues: 72
  loop : -0.50 (0.40), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 174 
 HIS   0.006   0.001   HIS B 199 
 PHE   0.042   0.002   PHE B 184 
 TYR   0.025   0.002   TYR C 211 
 ARG   0.021   0.001   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.40836 (  651)
  hydrogen bonds       : angle       5.29526 ( 1719)
  covalent geometry    : bond        0.00870 (10450)
  covalent geometry    : angle       2.03278 (14404)

*********************** 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
  414 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 359
  time to evaluate  : 0.897 
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   47 ILE cc_start: 0.9052 (mm) cc_final: 0.8826 (mp)
REVERT: B   65 TYR cc_start: 0.6524 (m-80) cc_final: 0.6015 (m-80)
REVERT: B   80 LYS cc_start: 0.8277 (mtmm) cc_final: 0.8017 (mtmm)
REVERT: B  110 TYR cc_start: 0.7317 (m-80) cc_final: 0.6947 (m-10)
REVERT: B  173 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7525 (m-70)
REVERT: B  180 MET cc_start: 0.8734 (mpp) cc_final: 0.8133 (mpp)
REVERT: B  194 LYS cc_start: 0.8870 (mttm) cc_final: 0.8661 (mttm)
REVERT: B  198 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9078 (mp)
REVERT: B  211 TYR cc_start: 0.7586 (m-80) cc_final: 0.7259 (m-80)
REVERT: B  257 LYS cc_start: 0.9013 (tppp) cc_final: 0.8737 (mmtm)
REVERT: B  276 TYR cc_start: 0.8887 (m-80) cc_final: 0.8671 (m-80)
REVERT: B  281 ARG cc_start: 0.8188 (tpp80) cc_final: 0.7823 (tpp-160)
REVERT: B  331 HIS cc_start: 0.7245 (t70) cc_final: 0.6993 (t-90)
REVERT: B  345 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8321 (mm-30)
REVERT: B  357 LYS cc_start: 0.8937 (mtmm) cc_final: 0.8596 (mtmm)
REVERT: B  382 ARG cc_start: 0.8571 (mmp80) cc_final: 0.8195 (mmp80)
REVERT: B  383 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8203 (tm-30)
REVERT: A   64 HIS cc_start: 0.8545 (t-90) cc_final: 0.8135 (t70)
REVERT: A   80 LYS cc_start: 0.8351 (mtmm) cc_final: 0.7905 (mtmm)
REVERT: A  153 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7288 (mm-30)
REVERT: A  194 LYS cc_start: 0.8942 (mttm) cc_final: 0.8486 (mttm)
REVERT: A  198 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9083 (mp)
REVERT: A  200 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7439 (mm-40)
REVERT: A  257 LYS cc_start: 0.9103 (tppp) cc_final: 0.8649 (tppp)
REVERT: A  259 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8329 (mm-30)
REVERT: A  337 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9040 (mm)
REVERT: A  345 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8348 (mm-30)
REVERT: A  354 GLU cc_start: 0.8575 (tp30) cc_final: 0.7863 (tt0)
REVERT: A  355 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8334 (pm20)
REVERT: A  357 LYS cc_start: 0.8622 (pttp) cc_final: 0.8252 (pttm)
REVERT: A  368 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8064 (tm-30)
REVERT: A  383 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8236 (tm-30)
REVERT: C   32 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8495 (tp-100)
REVERT: C   47 ILE cc_start: 0.9193 (mm) cc_final: 0.8831 (mp)
REVERT: C   64 HIS cc_start: 0.8557 (t-90) cc_final: 0.7944 (t-90)
REVERT: C   65 TYR cc_start: 0.6763 (m-80) cc_final: 0.6159 (m-80)
REVERT: C   80 LYS cc_start: 0.8568 (mtmm) cc_final: 0.7883 (mtmm)
REVERT: C   84 ASP cc_start: 0.8289 (m-30) cc_final: 0.8032 (m-30)
REVERT: C   87 TYR cc_start: 0.8688 (m-80) cc_final: 0.7752 (m-80)
REVERT: C   88 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7295 (mm-30)
REVERT: C  180 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8411 (mpp)
REVERT: C  194 LYS cc_start: 0.8707 (mttm) cc_final: 0.8345 (mttm)
REVERT: C  198 ILE cc_start: 0.9449 (OUTLIER) cc_final: 0.9188 (mp)
REVERT: C  255 LYS cc_start: 0.3477 (mmtt) cc_final: 0.2697 (tptt)
REVERT: C  308 THR cc_start: 0.6852 (m) cc_final: 0.6513 (m)
REVERT: C  357 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8684 (mtmm)
REVERT: C  365 GLN cc_start: 0.8862 (tp40) cc_final: 0.8562 (tp-100)
REVERT: C  383 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8117 (tm-30)
  outliers start: 55
  outliers final: 37
  residues processed: 384
  average time/residue: 0.3091
  time to fit residues: 159.4731
Evaluate side-chains
  388 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 344
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
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  148 ASP
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  175 LEU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   30 ASN
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   61 CYS
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  197 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  231 LYS
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  296 TYR
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  318 ASN
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  355 GLU
Chi-restraints excluded: chain C residue   23 LYS
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  180 MET
Chi-restraints excluded: chain C residue  197 LEU
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  282 VAL
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 113 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 66 optimal weight:    0.9990
   chunk 82 optimal weight:    8.9990
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 48 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9990
   chunk 105 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
B  74 ASN
B 217 ASN
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A   5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 380 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.174258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.147586 restraints weight = 19516.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.4018 rms_B_bonded: 3.84
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4018
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4018 r_free = 0.4018    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4016 r_free = 0.4016    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4016
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          1.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.196  10450  Z= 0.454
  Angle     :  2.034  70.132  14404  Z= 0.892
  Chirality :  0.220   4.451   1722
  Planarity :  0.006   0.063   1632
  Dihedral  : 21.885 178.673   1932
  Min Nonbonded Distance : 1.715

Molprobity Statistics.
  All-atom Clashscore : 39.46
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.53 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 29.77 %
    Favored  : 65.65 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.25), residues: 1125
  helix:  0.34 (0.18), residues: 759
  sheet: -2.36 (0.79), residues: 30
  loop : -0.54 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 174 
 HIS   0.008   0.001   HIS C 331 
 PHE   0.036   0.003   PHE B 184 
 TYR   0.018   0.002   TYR B 211 
 ARG   0.013   0.001   ARG A 339 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.40386 (  651)
  hydrogen bonds       : angle       5.34238 ( 1719)
  covalent geometry    : bond        0.00835 (10450)
  covalent geometry    : angle       2.03442 (14404)

*********************** 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
  381 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 336
  time to evaluate  : 1.033 
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: B   65 TYR cc_start: 0.6473 (m-80) cc_final: 0.6018 (m-80)
REVERT: B   80 LYS cc_start: 0.8232 (mtmm) cc_final: 0.8031 (mtmm)
REVERT: B  110 TYR cc_start: 0.7275 (m-80) cc_final: 0.6972 (m-10)
REVERT: B  118 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8482 (ptpt)
REVERT: B  173 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7475 (m-70)
REVERT: B  180 MET cc_start: 0.8631 (mpp) cc_final: 0.8117 (mpp)
REVERT: B  198 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.9061 (mp)
REVERT: B  211 TYR cc_start: 0.7542 (m-80) cc_final: 0.7278 (m-80)
REVERT: B  276 TYR cc_start: 0.8764 (m-80) cc_final: 0.8549 (m-80)
REVERT: B  281 ARG cc_start: 0.8171 (tpp80) cc_final: 0.7806 (tpp-160)
REVERT: B  345 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8199 (mm-30)
REVERT: B  357 LYS cc_start: 0.8895 (mtmm) cc_final: 0.8624 (mtmm)
REVERT: B  382 ARG cc_start: 0.8582 (mmp80) cc_final: 0.8213 (mmp80)
REVERT: A   64 HIS cc_start: 0.8444 (t-90) cc_final: 0.8067 (t70)
REVERT: A  194 LYS cc_start: 0.8951 (mttm) cc_final: 0.8436 (mttm)
REVERT: A  198 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9058 (mp)
REVERT: A  200 GLN cc_start: 0.7687 (mm-40) cc_final: 0.7438 (mm-40)
REVERT: A  251 VAL cc_start: 0.9161 (m) cc_final: 0.8926 (m)
REVERT: A  252 ARG cc_start: 0.8131 (mmt90) cc_final: 0.7529 (mmt90)
REVERT: A  257 LYS cc_start: 0.9079 (tppp) cc_final: 0.8628 (tppp)
REVERT: A  259 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8313 (mm-30)
REVERT: A  337 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9061 (mm)
REVERT: A  345 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8370 (mm-30)
REVERT: A  354 GLU cc_start: 0.8578 (tp30) cc_final: 0.7826 (tt0)
REVERT: A  356 ARG cc_start: 0.7873 (mmt-90) cc_final: 0.7412 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8614 (pttp) cc_final: 0.8243 (pttm)
REVERT: A  368 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8016 (tm-30)
REVERT: A  383 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8311 (tm-30)
REVERT: C   47 ILE cc_start: 0.9165 (mm) cc_final: 0.8828 (mp)
REVERT: C   65 TYR cc_start: 0.6672 (m-80) cc_final: 0.6135 (m-80)
REVERT: C   81 TYR cc_start: 0.8403 (t80) cc_final: 0.8113 (t80)
REVERT: C   84 ASP cc_start: 0.8294 (m-30) cc_final: 0.8031 (m-30)
REVERT: C  134 LEU cc_start: 0.9216 (mt) cc_final: 0.8654 (mt)
REVERT: C  180 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8426 (mpp)
REVERT: C  194 LYS cc_start: 0.8758 (mttm) cc_final: 0.8358 (mttm)
REVERT: C  198 ILE cc_start: 0.9428 (OUTLIER) cc_final: 0.9173 (mp)
REVERT: C  255 LYS cc_start: 0.3609 (mmtt) cc_final: 0.2852 (tptt)
REVERT: C  281 ARG cc_start: 0.8533 (tpp80) cc_final: 0.8286 (tpp80)
REVERT: C  308 THR cc_start: 0.6968 (m) cc_final: 0.6671 (m)
REVERT: C  357 LYS cc_start: 0.9017 (mtpp) cc_final: 0.8728 (mtmm)
REVERT: C  365 GLN cc_start: 0.8767 (tp40) cc_final: 0.8488 (tp-100)
REVERT: C  382 ARG cc_start: 0.8380 (mmp80) cc_final: 0.8113 (mmp-170)
REVERT: C  383 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8338 (tm-30)
  outliers start: 45
  outliers final: 31
  residues processed: 359
  average time/residue: 0.2727
  time to fit residues: 129.0074
Evaluate side-chains
  367 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 330
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
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  175 LEU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  338 GLN
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   30 ASN
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  296 TYR
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  318 ASN
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  180 MET
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  282 VAL
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 64 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0010
   chunk 59 optimal weight:    0.9980
   chunk 63 optimal weight:    0.4980
   chunk 42 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 71 optimal weight:    6.9990
   chunk 79 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
B  74 ASN
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 318 ASN
** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 GLN
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 324 GLN
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 380 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.177285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.150602 restraints weight = 19596.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.4064 rms_B_bonded: 3.92
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4064
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4064 r_free = 0.4064    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 = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4063
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7187
moved from start:          1.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.198  10450  Z= 0.448
  Angle     :  2.017  69.086  14404  Z= 0.888
  Chirality :  0.210   4.416   1722
  Planarity :  0.007   0.089   1632
  Dihedral  : 21.980 175.001   1932
  Min Nonbonded Distance : 1.701

Molprobity Statistics.
  All-atom Clashscore : 37.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 30.38 %
    Favored  : 65.85 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.25), residues: 1125
  helix:  0.34 (0.19), residues: 735
  sheet: -2.59 (0.76), residues: 30
  loop : -0.58 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 174 
 HIS   0.008   0.001   HIS A 331 
 PHE   0.026   0.002   PHE B 184 
 TYR   0.021   0.002   TYR A 323 
 ARG   0.013   0.001   ARG A 339 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.40358 (  651)
  hydrogen bonds       : angle       5.38384 ( 1719)
  covalent geometry    : bond        0.00825 (10450)
  covalent geometry    : angle       2.01675 (14404)

********************** 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
  375 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 338
  time to evaluate  : 1.073 
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: 0.7336 (mt-10) cc_final: 0.6988 (mt-10)
REVERT: B   65 TYR cc_start: 0.6474 (m-80) cc_final: 0.5993 (m-80)
REVERT: B   80 LYS cc_start: 0.8283 (mtmm) cc_final: 0.7863 (mtmm)
REVERT: B  110 TYR cc_start: 0.7253 (m-80) cc_final: 0.6917 (m-10)
REVERT: B  118 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8420 (ptpt)
REVERT: B  173 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.7424 (m-70)
REVERT: B  180 MET cc_start: 0.8623 (mpp) cc_final: 0.8069 (mpp)
REVERT: B  194 LYS cc_start: 0.8506 (mttm) cc_final: 0.8054 (mmtm)
REVERT: B  198 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.9067 (mp)
REVERT: B  211 TYR cc_start: 0.7459 (m-80) cc_final: 0.7223 (m-80)
REVERT: B  281 ARG cc_start: 0.8150 (tpp80) cc_final: 0.7788 (tpp-160)
REVERT: B  345 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8254 (mm-30)
REVERT: B  357 LYS cc_start: 0.8912 (mtmm) cc_final: 0.8485 (mtmm)
REVERT: B  360 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7835 (mt-10)
REVERT: B  382 ARG cc_start: 0.8548 (mmp80) cc_final: 0.8212 (mmp80)
REVERT: A   64 HIS cc_start: 0.8413 (t-90) cc_final: 0.8022 (t70)
REVERT: A  149 ARG cc_start: 0.7570 (mmm-85) cc_final: 0.7126 (mmm-85)
REVERT: A  200 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7410 (mm-40)
REVERT: A  259 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8338 (mm-30)
REVERT: A  284 ASN cc_start: 0.8071 (m110) cc_final: 0.7809 (m-40)
REVERT: A  337 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.8993 (mm)
REVERT: A  345 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8494 (mm-30)
REVERT: A  354 GLU cc_start: 0.8489 (tp30) cc_final: 0.8221 (pt0)
REVERT: A  356 ARG cc_start: 0.7979 (mmt-90) cc_final: 0.7339 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8613 (pttp) cc_final: 0.8169 (pttm)
REVERT: A  368 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7942 (tm-30)
REVERT: A  383 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8288 (tm-30)
REVERT: C   47 ILE cc_start: 0.9113 (mm) cc_final: 0.8821 (mp)
REVERT: C   65 TYR cc_start: 0.6685 (m-80) cc_final: 0.6105 (m-80)
REVERT: C   84 ASP cc_start: 0.8354 (m-30) cc_final: 0.8051 (m-30)
REVERT: C  134 LEU cc_start: 0.9236 (mt) cc_final: 0.8671 (mt)
REVERT: C  194 LYS cc_start: 0.8618 (mttm) cc_final: 0.8278 (mttm)
REVERT: C  198 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9186 (mp)
REVERT: C  255 LYS cc_start: 0.3553 (mmtt) cc_final: 0.2827 (tptt)
REVERT: C  281 ARG cc_start: 0.8508 (tpp80) cc_final: 0.8289 (tpp80)
REVERT: C  324 GLN cc_start: 0.6353 (mm110) cc_final: 0.6017 (mm-40)
REVERT: C  357 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8667 (mtmm)
REVERT: C  365 GLN cc_start: 0.8698 (tp40) cc_final: 0.8433 (tp-100)
REVERT: C  383 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8341 (tm-30)
  outliers start: 37
  outliers final: 27
  residues processed: 353
  average time/residue: 0.3665
  time to fit residues: 172.7826
Evaluate side-chains
  351 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 320
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
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  148 ASP
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  343 HIS
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   59 THR
Chi-restraints excluded: chain A residue  103 VAL
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  231 LYS
Chi-restraints excluded: chain A residue  296 TYR
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain C residue   23 LYS
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  282 VAL
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 111 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 103 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** 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**
** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 347 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 = 0.4361 r_free = 0.4361 target = 0.176283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.149741 restraints weight = 19454.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.4050 rms_B_bonded: 3.90
r_work (final): 0.4050
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4050
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4050 r_free = 0.4050    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4050 r_free = 0.4050    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4050
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          1.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.199  10450  Z= 0.441
  Angle     :  1.983  68.654  14404  Z= 0.865
  Chirality :  0.203   4.429   1722
  Planarity :  0.007   0.062   1632
  Dihedral  : 21.818 178.618   1932
  Min Nonbonded Distance : 1.697

Molprobity Statistics.
  All-atom Clashscore : 36.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 30.99 %
    Favored  : 65.44 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.25), residues: 1125
  helix:  0.32 (0.19), residues: 741
  sheet: -2.21 (0.53), residues: 72
  loop : -0.36 (0.39), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 174 
 HIS   0.005   0.001   HIS B 331 
 PHE   0.032   0.002   PHE B 184 
 TYR   0.019   0.002   TYR A 323 
 ARG   0.020   0.001   ARG A 327 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.40468 (  651)
  hydrogen bonds       : angle       5.36996 ( 1719)
  covalent geometry    : bond        0.00821 (10450)
  covalent geometry    : angle       1.98294 (14404)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6541.86 seconds
wall clock time: 116 minutes 40.74 seconds (7000.74 seconds total)