Starting phenix.real_space_refine
on Fri Feb 14 10:50:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fvd_50803/02_2025/9fvd_50803.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fvd_50803/02_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_50803/02_2025/9fvd_50803.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fvd_50803/02_2025/9fvd_50803.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fvd_50803/02_2025/9fvd_50803.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fvd_50803/02_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-5592/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: 8.36, per 1000 atoms: 0.82
  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: 4.15
  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: 5.37
  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: 3.64

  Time building geometry restraints manager: 4.46 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:             15.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     33.500
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.590
-------------------------------------------------------------------------------
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= 0.212
  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 

*********************** 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  : 1.162 
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: 0.3118
  time to fit residues: 154.8506
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  : 1.089 
-------------------------------------------------------------------------------
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 = 34)----------------|
| 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: 0.3929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3929 r_free = 0.3929    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3917 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= 1.178
  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 : 45.52
  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 

*********************** 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  : 1.121 
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: 0.8479 (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: 0.8263 (mm-30)
REVERT: B  357 LYS cc_start: 0.8788 (mtmm) cc_final: 0.8208 (mtmt)
REVERT: B  380 GLN cc_start: 0.8600 (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: 0.8856 (pm20)
REVERT: A  323 TYR cc_start: 0.8905 (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: 0.8531 (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: 0.8663 (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: 0.2897
  time to fit residues: 149.7800
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  : 1.108 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.9988

-------------------------------------------------------------------------------
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 = 0.4261 r_free = 0.4261 target = 0.170508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.145764 restraints weight = 19491.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3997 rms_B_bonded: 3.85
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3997
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3997 r_free = 0.3997    target_work(ls_wunit_k1) = 0.153         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3993 r_free = 0.3993    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3993
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.9165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.197  10450  Z= 0.765
  Angle     :  2.682  71.046  14404  Z= 1.203
  Chirality :  0.317   4.669   1722
  Planarity :  0.008   0.092   1632
  Dihedral  : 20.849 172.006   1932
  Min Nonbonded Distance : 1.757

Molprobity Statistics.
  All-atom Clashscore : 44.25
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.71 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 17.84 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  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:  0.46 (0.25), residues: 1125
  helix:  1.23 (0.19), residues: 720
  sheet: -2.33 (0.88), 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   0.032   0.002   TYR C 323 
 ARG   0.019   0.001   ARG A 327 

*********************** 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
  448 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 391
  time to evaluate  : 1.118 
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: B   65 TYR cc_start: 0.6517 (m-80) cc_final: 0.6233 (m-80)
REVERT: B   88 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7879 (mm-30)
REVERT: B  133 PHE cc_start: 0.8701 (t80) cc_final: 0.8459 (t80)
REVERT: B  134 LEU cc_start: 0.9286 (mt) cc_final: 0.8820 (mt)
REVERT: B  148 ASP cc_start: 0.6819 (p0) cc_final: 0.6380 (p0)
REVERT: B  152 ILE cc_start: 0.8745 (pt) cc_final: 0.8543 (pt)
REVERT: B  153 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7670 (mm-30)
REVERT: B  180 MET cc_start: 0.8767 (mpp) cc_final: 0.8547 (mpp)
REVERT: B  198 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9026 (mp)
REVERT: B  252 ARG cc_start: 0.8157 (mmt90) cc_final: 0.7880 (mmt90)
REVERT: B  259 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7788 (mm-30)
REVERT: B  308 THR cc_start: 0.7624 (m) cc_final: 0.7333 (m)
REVERT: B  319 VAL cc_start: 0.3522 (OUTLIER) cc_final: 0.3294 (t)
REVERT: B  323 TYR cc_start: 0.8583 (m-80) cc_final: 0.8137 (m-80)
REVERT: B  345 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8300 (mm-30)
REVERT: B  356 ARG cc_start: 0.7766 (mmt-90) cc_final: 0.7414 (mmt-90)
REVERT: B  380 GLN cc_start: 0.8791 (tp40) cc_final: 0.8554 (tp40)
REVERT: B  383 GLU cc_start: 0.8602 (tm-30) cc_final: 0.8251 (tm-30)
REVERT: A    2 MET cc_start: 0.8486 (ppp) cc_final: 0.8213 (ppp)
REVERT: A   44 ASN cc_start: 0.9085 (p0) cc_final: 0.8633 (p0)
REVERT: A   65 TYR cc_start: 0.5616 (m-80) cc_final: 0.5155 (m-80)
REVERT: A   80 LYS cc_start: 0.8347 (mtmm) cc_final: 0.7876 (mtmm)
REVERT: A   81 TYR cc_start: 0.8558 (t80) cc_final: 0.8342 (t80)
REVERT: A   84 ASP cc_start: 0.7962 (m-30) cc_final: 0.7687 (m-30)
REVERT: A  157 ARG cc_start: 0.8591 (ttm170) cc_final: 0.8383 (ttp80)
REVERT: A  198 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9073 (mp)
REVERT: A  200 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7485 (mm-40)
REVERT: A  252 ARG cc_start: 0.8198 (mmt90) cc_final: 0.7990 (mmt90)
REVERT: A  288 ILE cc_start: 0.8537 (tp) cc_final: 0.8121 (tp)
REVERT: A  290 ASN cc_start: 0.8586 (m-40) cc_final: 0.8373 (m-40)
REVERT: A  308 THR cc_start: 0.8149 (m) cc_final: 0.7296 (m)
REVERT: A  337 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8858 (mm)
REVERT: A  345 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8190 (mm-30)
REVERT: A  354 GLU cc_start: 0.8747 (tp30) cc_final: 0.8469 (pt0)
REVERT: A  356 ARG cc_start: 0.7535 (mmt-90) cc_final: 0.7015 (mmt-90)
REVERT: A  361 GLN cc_start: 0.8757 (tp40) cc_final: 0.8512 (tm-30)
REVERT: A  380 GLN cc_start: 0.8521 (tp-100) cc_final: 0.8259 (tp40)
REVERT: A  383 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8097 (tm-30)
REVERT: A  385 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8494 (mt)
REVERT: C   32 GLN cc_start: 0.8807 (tp-100) cc_final: 0.8525 (tp-100)
REVERT: C   37 ASN cc_start: 0.9138 (m-40) cc_final: 0.8917 (m-40)
REVERT: C   64 HIS cc_start: 0.8772 (t-90) cc_final: 0.8524 (t-90)
REVERT: C   80 LYS cc_start: 0.8470 (mtmm) cc_final: 0.7945 (mtmm)
REVERT: C   87 TYR cc_start: 0.8739 (m-80) cc_final: 0.8531 (m-80)
REVERT: C  180 MET cc_start: 0.8748 (mpp) cc_final: 0.8499 (mpp)
REVERT: C  198 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9014 (mp)
REVERT: C  234 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.8928 (mm)
REVERT: C  247 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8732 (tp)
REVERT: C  252 ARG cc_start: 0.8130 (mmt90) cc_final: 0.7830 (mmt90)
REVERT: C  308 THR cc_start: 0.8012 (m) cc_final: 0.7778 (m)
REVERT: C  345 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8230 (mm-30)
REVERT: C  356 ARG cc_start: 0.7536 (mmt-90) cc_final: 0.6838 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8941 (mtmm) cc_final: 0.8400 (mtmm)
REVERT: C  380 GLN cc_start: 0.8647 (tp40) cc_final: 0.8389 (tp40)
REVERT: C  383 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8098 (tm-30)
  outliers start: 57
  outliers final: 23
  residues processed: 422
  average time/residue: 0.2732
  time to fit residues: 152.4273
Evaluate side-chains
  384 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 353
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
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  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:   10.0000
   chunk 110 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 92 optimal weight:    4.9990
   chunk 94 optimal weight:    0.9980
   chunk 114 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0980
   chunk 41 optimal weight:    5.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 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 = 0.4274 r_free = 0.4274 target = 0.171438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.145881 restraints weight = 19481.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 3.97
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3975
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3975 r_free = 0.3975    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 = 0.3970 r_free = 0.3970    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3970
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.9969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.207  10450  Z= 0.660
  Angle     :  2.320  70.098  14404  Z= 1.042
  Chirality :  0.306   4.620   1722
  Planarity :  0.007   0.089   1632
  Dihedral  : 22.017 174.353   1932
  Min Nonbonded Distance : 1.755

Molprobity Statistics.
  All-atom Clashscore : 41.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 22.43 %
    Favored  : 72.38 %
  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:  0.45 (0.25), residues: 1125
  helix:  1.19 (0.19), residues: 717
  sheet: -2.46 (0.85), residues: 30
  loop : -1.14 (0.32), residues: 378

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   0.019   0.002   PHE B  27 
 TYR   0.031   0.002   TYR A 323 
 ARG   0.004   0.001   ARG C 188 

*********************** 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
  433 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 382
  time to evaluate  : 1.078 
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: B   65 TYR cc_start: 0.6791 (m-80) cc_final: 0.6357 (m-80)
REVERT: B   80 LYS cc_start: 0.8500 (mtmm) cc_final: 0.8064 (mtmm)
REVERT: B   83 ARG cc_start: 0.8144 (mmp-170) cc_final: 0.7938 (mmp-170)
REVERT: B   88 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7770 (mm-30)
REVERT: B  133 PHE cc_start: 0.8758 (t80) cc_final: 0.8557 (t80)
REVERT: B  148 ASP cc_start: 0.6562 (p0) cc_final: 0.5934 (p0)
REVERT: B  180 MET cc_start: 0.8855 (mpp) cc_final: 0.8600 (mpp)
REVERT: B  184 PHE cc_start: 0.9114 (t80) cc_final: 0.8898 (t80)
REVERT: B  194 LYS cc_start: 0.8982 (mttm) cc_final: 0.8413 (mttm)
REVERT: B  198 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9097 (mp)
REVERT: B  234 LEU cc_start: 0.9434 (mt) cc_final: 0.9223 (mt)
REVERT: B  331 HIS cc_start: 0.6859 (t70) cc_final: 0.6485 (t-90)
REVERT: B  345 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8393 (mm-30)
REVERT: B  357 LYS cc_start: 0.9043 (mtmm) cc_final: 0.8715 (mtmm)
REVERT: B  365 GLN cc_start: 0.8799 (tp40) cc_final: 0.8456 (tp-100)
REVERT: B  382 ARG cc_start: 0.8413 (mmp80) cc_final: 0.8176 (mmp-170)
REVERT: B  383 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8236 (tm-30)
REVERT: A   44 ASN cc_start: 0.9108 (p0) cc_final: 0.8602 (p0)
REVERT: A   47 ILE cc_start: 0.9095 (mm) cc_final: 0.8831 (mp)
REVERT: A   65 TYR cc_start: 0.6074 (m-80) cc_final: 0.5585 (m-80)
REVERT: A   80 LYS cc_start: 0.8326 (mtmm) cc_final: 0.7866 (mtmm)
REVERT: A   84 ASP cc_start: 0.8003 (m-30) cc_final: 0.7705 (m-30)
REVERT: A  163 GLN cc_start: 0.8405 (pt0) cc_final: 0.8033 (pp30)
REVERT: A  198 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9095 (mp)
REVERT: A  259 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8156 (mm-30)
REVERT: A  337 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8995 (mm)
REVERT: A  345 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8242 (mm-30)
REVERT: A  354 GLU cc_start: 0.8388 (tp30) cc_final: 0.7986 (tt0)
REVERT: A  356 ARG cc_start: 0.7629 (mmt-90) cc_final: 0.7116 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8673 (pttp) cc_final: 0.8159 (ptpp)
REVERT: A  361 GLN cc_start: 0.8736 (tp40) cc_final: 0.8504 (tm-30)
REVERT: A  380 GLN cc_start: 0.8612 (tp-100) cc_final: 0.8260 (tp40)
REVERT: A  383 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8117 (tm-30)
REVERT: C   32 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8560 (tp-100)
REVERT: C   47 ILE cc_start: 0.9186 (mm) cc_final: 0.8830 (mp)
REVERT: C   64 HIS cc_start: 0.8641 (t-90) cc_final: 0.8174 (t-90)
REVERT: C   65 TYR cc_start: 0.6510 (m-80) cc_final: 0.6126 (m-80)
REVERT: C   80 LYS cc_start: 0.8462 (mtmm) cc_final: 0.8045 (mtmm)
REVERT: C  165 GLN cc_start: 0.5840 (OUTLIER) cc_final: 0.5465 (mt0)
REVERT: C  173 HIS cc_start: 0.8048 (t-90) cc_final: 0.7759 (t-90)
REVERT: C  198 ILE cc_start: 0.9422 (OUTLIER) cc_final: 0.9115 (mp)
REVERT: C  211 TYR cc_start: 0.7514 (m-80) cc_final: 0.7294 (m-80)
REVERT: C  234 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9141 (mm)
REVERT: C  247 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8785 (tp)
REVERT: C  252 ARG cc_start: 0.8308 (mmt90) cc_final: 0.7845 (mmt90)
REVERT: C  308 THR cc_start: 0.7929 (m) cc_final: 0.7701 (m)
REVERT: C  345 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8283 (mm-30)
REVERT: C  356 ARG cc_start: 0.7565 (mmt-90) cc_final: 0.7178 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8843 (mtmm) cc_final: 0.8336 (mtmm)
REVERT: C  365 GLN cc_start: 0.8889 (tp40) cc_final: 0.8552 (tp-100)
REVERT: C  383 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8150 (tm-30)
  outliers start: 51
  outliers final: 22
  residues processed: 407
  average time/residue: 0.2911
  time to fit residues: 154.9272
Evaluate side-chains
  378 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 349
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
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  361 GLN
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  186 ILE
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   30 ASN
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  165 GLN
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  198 ILE
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:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 71 optimal weight:    5.9990
   chunk 116 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 82 optimal weight:    9.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 GLN
** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 GLN
** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 318 ASN
** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
** 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.173071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.146897 restraints weight = 19656.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 4.04
r_work (final): 0.3994
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3996
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3996 r_free = 0.3996    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 = 0.3996 r_free = 0.3996    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          1.0728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.202  10450  Z= 0.601
  Angle     :  2.249  70.691  14404  Z= 1.005
  Chirality :  0.269   4.639   1722
  Planarity :  0.007   0.119   1632
  Dihedral  : 22.395 172.850   1932
  Min Nonbonded Distance : 1.750

Molprobity Statistics.
  All-atom Clashscore : 40.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 23.45 %
    Favored  : 70.64 %
  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:  0.42 (0.26), residues: 1125
  helix:  1.08 (0.19), residues: 720
  sheet: -1.23 (0.56), residues: 72
  loop : -1.03 (0.36), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 174 
 HIS   0.006   0.001   HIS B 162 
 PHE   0.031   0.002   PHE A 184 
 TYR   0.020   0.002   TYR B 211 
 ARG   0.018   0.001   ARG C 382 

*********************** 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
  439 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 381
  time to evaluate  : 0.881 
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: 0.6836 (m-80) cc_final: 0.6291 (m-80)
REVERT: B   80 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8225 (mtmm)
REVERT: B   88 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7899 (mm-30)
REVERT: B  148 ASP cc_start: 0.6535 (p0) cc_final: 0.6157 (p0)
REVERT: B  168 VAL cc_start: 0.6609 (m) cc_final: 0.6382 (m)
REVERT: B  173 HIS cc_start: 0.7997 (OUTLIER) cc_final: 0.7619 (m-70)
REVERT: B  181 LYS cc_start: 0.8605 (tptt) cc_final: 0.8351 (tptp)
REVERT: B  198 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9057 (mp)
REVERT: B  211 TYR cc_start: 0.7236 (m-80) cc_final: 0.6983 (m-10)
REVERT: B  257 LYS cc_start: 0.8931 (tppp) cc_final: 0.8556 (mmtp)
REVERT: B  259 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7758 (mm-30)
REVERT: B  331 HIS cc_start: 0.7257 (t70) cc_final: 0.7053 (t-90)
REVERT: B  345 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8385 (mm-30)
REVERT: B  357 LYS cc_start: 0.9052 (mtmm) cc_final: 0.8781 (mtmt)
REVERT: B  365 GLN cc_start: 0.8792 (tp40) cc_final: 0.8454 (tp-100)
REVERT: B  380 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8578 (tp-100)
REVERT: B  383 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8270 (tm-30)
REVERT: A   64 HIS cc_start: 0.8693 (t-90) cc_final: 0.8271 (t70)
REVERT: A   65 TYR cc_start: 0.6242 (m-80) cc_final: 0.5796 (m-80)
REVERT: A   80 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7862 (mtmm)
REVERT: A   84 ASP cc_start: 0.8089 (m-30) cc_final: 0.7805 (m-30)
REVERT: A  198 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.9068 (mp)
REVERT: A  252 ARG cc_start: 0.8130 (mmt90) cc_final: 0.7499 (mmt90)
REVERT: A  257 LYS cc_start: 0.8994 (tppp) cc_final: 0.8511 (tppp)
REVERT: A  337 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9033 (mm)
REVERT: A  345 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8306 (mm-30)
REVERT: A  352 ASP cc_start: 0.8604 (p0) cc_final: 0.8219 (p0)
REVERT: A  354 GLU cc_start: 0.8387 (tp30) cc_final: 0.8143 (pt0)
REVERT: A  356 ARG cc_start: 0.7706 (mmt-90) cc_final: 0.7274 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8666 (pttp) cc_final: 0.8163 (ptpp)
REVERT: A  383 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8169 (tm-30)
REVERT: A  385 LEU cc_start: 0.8595 (mm) cc_final: 0.8393 (mt)
REVERT: C   32 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8516 (tp-100)
REVERT: C   54 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8009 (mm-30)
REVERT: C   64 HIS cc_start: 0.8562 (t-90) cc_final: 0.8312 (t-90)
REVERT: C   65 TYR cc_start: 0.6626 (m-80) cc_final: 0.6358 (m-80)
REVERT: C   80 LYS cc_start: 0.8486 (mtmm) cc_final: 0.7786 (mtmm)
REVERT: C   84 ASP cc_start: 0.8297 (m-30) cc_final: 0.7975 (m-30)
REVERT: C  180 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8627 (mpp)
REVERT: C  198 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9127 (mp)
REVERT: C  234 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9126 (mm)
REVERT: C  252 ARG cc_start: 0.8328 (mmt90) cc_final: 0.8054 (mmt90)
REVERT: C  308 THR cc_start: 0.7630 (m) cc_final: 0.7079 (m)
REVERT: C  324 GLN cc_start: 0.7295 (mm-40) cc_final: 0.6879 (mm-40)
REVERT: C  356 ARG cc_start: 0.7707 (mmt-90) cc_final: 0.7154 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8953 (mtmm) cc_final: 0.8468 (mtmm)
REVERT: C  365 GLN cc_start: 0.8888 (tp40) cc_final: 0.8546 (tp-100)
REVERT: C  383 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8346 (tm-30)
  outliers start: 58
  outliers final: 31
  residues processed: 407
  average time/residue: 0.2769
  time to fit residues: 147.3332
Evaluate side-chains
  364 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 326
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   48 ASP
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  186 ILE
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 A residue   48 ASP
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  209 ASP
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   31 HIS
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  144 LEU
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  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  323 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9990
   chunk 90 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0980
   chunk 64 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   overall best weight:    1.4188

-------------------------------------------------------------------------------
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 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 338 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.174002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.148040 restraints weight = 19603.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.4004 rms_B_bonded: 3.95
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4004 r_free = 0.4004    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4003 r_free = 0.4003    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4003
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start:          1.1332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.199  10450  Z= 0.574
  Angle     :  2.094  70.755  14404  Z= 0.935
  Chirality :  0.250   4.643   1722
  Planarity :  0.007   0.108   1632
  Dihedral  : 21.990 170.384   1932
  Min Nonbonded Distance : 1.744

Molprobity Statistics.
  All-atom Clashscore : 41.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 25.18 %
    Favored  : 68.30 %
  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:  0.32 (0.26), residues: 1125
  helix:  0.81 (0.19), residues: 753
  sheet: -1.31 (0.56), residues: 72
  loop : -0.69 (0.39), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 174 
 HIS   0.007   0.001   HIS C 331 
 PHE   0.039   0.002   PHE B 184 
 TYR   0.022   0.002   TYR A 323 
 ARG   0.011   0.001   ARG A 339 

*********************** 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
  418 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 354
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 ILE cc_start: 0.9076 (mm) cc_final: 0.8835 (mp)
REVERT: B   65 TYR cc_start: 0.6710 (m-80) cc_final: 0.6101 (m-80)
REVERT: B   80 LYS cc_start: 0.8573 (mtmm) cc_final: 0.7986 (mtmm)
REVERT: B   84 ASP cc_start: 0.8153 (m-30) cc_final: 0.7934 (m-30)
REVERT: B   88 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7874 (mm-30)
REVERT: B  110 TYR cc_start: 0.7368 (m-80) cc_final: 0.7012 (m-10)
REVERT: B  148 ASP cc_start: 0.6583 (p0) cc_final: 0.6184 (p0)
REVERT: B  173 HIS cc_start: 0.7986 (OUTLIER) cc_final: 0.7588 (m-70)
REVERT: B  198 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9028 (mp)
REVERT: B  204 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7867 (tt)
REVERT: B  211 TYR cc_start: 0.7396 (m-80) cc_final: 0.7071 (m-80)
REVERT: B  257 LYS cc_start: 0.9052 (tppp) cc_final: 0.8704 (mmtp)
REVERT: B  331 HIS cc_start: 0.7288 (t70) cc_final: 0.7075 (t-90)
REVERT: B  334 GLU cc_start: 0.8618 (tp30) cc_final: 0.8359 (tp30)
REVERT: B  345 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8347 (mm-30)
REVERT: B  357 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8804 (mtmt)
REVERT: B  365 GLN cc_start: 0.8753 (tp40) cc_final: 0.8420 (tp-100)
REVERT: B  382 ARG cc_start: 0.8669 (mmp80) cc_final: 0.8460 (mmp-170)
REVERT: B  383 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8230 (tm-30)
REVERT: A   47 ILE cc_start: 0.9097 (mm) cc_final: 0.8853 (mp)
REVERT: A   64 HIS cc_start: 0.8611 (t-90) cc_final: 0.8231 (t-90)
REVERT: A   80 LYS cc_start: 0.8298 (mtmm) cc_final: 0.7804 (mtmm)
REVERT: A   81 TYR cc_start: 0.8429 (t80) cc_final: 0.8176 (t80)
REVERT: A   83 ARG cc_start: 0.8151 (mmp-170) cc_final: 0.7868 (mmp-170)
REVERT: A   84 ASP cc_start: 0.8117 (m-30) cc_final: 0.7793 (m-30)
REVERT: A  198 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9085 (mp)
REVERT: A  257 LYS cc_start: 0.9033 (tppp) cc_final: 0.8779 (mmmm)
REVERT: A  337 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9028 (mm)
REVERT: A  345 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8303 (mm-30)
REVERT: A  352 ASP cc_start: 0.8529 (p0) cc_final: 0.8327 (p0)
REVERT: A  354 GLU cc_start: 0.8368 (tp30) cc_final: 0.8157 (pt0)
REVERT: A  357 LYS cc_start: 0.8663 (pttp) cc_final: 0.8105 (ptpp)
REVERT: C    3 ASP cc_start: 0.8557 (t0) cc_final: 0.8276 (t0)
REVERT: C   32 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8557 (tp-100)
REVERT: C   47 ILE cc_start: 0.9161 (mm) cc_final: 0.8828 (mp)
REVERT: C   64 HIS cc_start: 0.8578 (t-90) cc_final: 0.8344 (t-90)
REVERT: C   65 TYR cc_start: 0.6684 (m-80) cc_final: 0.6327 (m-80)
REVERT: C   84 ASP cc_start: 0.8324 (m-30) cc_final: 0.8027 (m-30)
REVERT: C   87 TYR cc_start: 0.8826 (m-80) cc_final: 0.8605 (m-80)
REVERT: C  180 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8564 (mpp)
REVERT: C  194 LYS cc_start: 0.8789 (mttm) cc_final: 0.8414 (mttm)
REVERT: C  198 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9138 (mp)
REVERT: C  211 TYR cc_start: 0.7385 (m-80) cc_final: 0.7157 (m-10)
REVERT: C  308 THR cc_start: 0.7849 (m) cc_final: 0.7405 (m)
REVERT: C  324 GLN cc_start: 0.6997 (mm-40) cc_final: 0.6657 (mm-40)
REVERT: C  357 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8335 (mtmm)
REVERT: C  365 GLN cc_start: 0.8915 (tp40) cc_final: 0.8589 (tp-100)
REVERT: C  382 ARG cc_start: 0.8531 (mmp80) cc_final: 0.8067 (mmp-170)
REVERT: C  383 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8239 (tm-30)
  outliers start: 64
  outliers final: 39
  residues processed: 380
  average time/residue: 0.2659
  time to fit residues: 134.9169
Evaluate side-chains
  387 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 341
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   48 ASP
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue  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  204 LEU
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  296 TYR
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  346 ILE
Chi-restraints excluded: chain B residue  361 GLN
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain A residue   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  144 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  255 LYS
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain C residue   23 LYS
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue   31 HIS
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain C residue  144 LEU
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  216 SER
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  257 LYS
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  282 VAL
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:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 84 optimal weight:    5.9990
   chunk 71 optimal weight:    0.5980
   chunk 90 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   chunk 60 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  74 ASN
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 298 GLN
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 ASN
** C 221 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 = 0.4363 r_free = 0.4363 target = 0.176753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.150389 restraints weight = 19625.572|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 3.87
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4063
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4063 r_free = 0.4063    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4064 r_free = 0.4064    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4064
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          1.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.192  10450  Z= 0.552
  Angle     :  2.052  72.288  14404  Z= 0.909
  Chirality :  0.226   4.488   1722
  Planarity :  0.007   0.107   1632
  Dihedral  : 21.766 166.710   1932
  Min Nonbonded Distance : 1.752

Molprobity Statistics.
  All-atom Clashscore : 39.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 26.81 %
    Favored  : 67.48 %
  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:  0.30 (0.25), residues: 1125
  helix:  0.79 (0.19), residues: 744
  sheet: -1.41 (0.54), residues: 72
  loop : -0.62 (0.38), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 174 
 HIS   0.008   0.001   HIS A 331 
 PHE   0.050   0.003   PHE A 184 
 TYR   0.027   0.002   TYR A 323 
 ARG   0.012   0.001   ARG B 327 

*********************** 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
  393 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 337
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLU cc_start: 0.7480 (mt-10) cc_final: 0.7208 (mt-10)
REVERT: B   65 TYR cc_start: 0.6554 (m-80) cc_final: 0.5982 (m-80)
REVERT: B   80 LYS cc_start: 0.8525 (mtmm) cc_final: 0.8259 (mtmm)
REVERT: B  110 TYR cc_start: 0.7219 (m-80) cc_final: 0.6865 (m-10)
REVERT: B  118 LYS cc_start: 0.8740 (mmmt) cc_final: 0.8479 (ptpt)
REVERT: B  148 ASP cc_start: 0.6451 (p0) cc_final: 0.6200 (p0)
REVERT: B  173 HIS cc_start: 0.7811 (OUTLIER) cc_final: 0.7388 (m-70)
REVERT: B  180 MET cc_start: 0.8764 (mpp) cc_final: 0.8351 (mpp)
REVERT: B  194 LYS cc_start: 0.8787 (mttm) cc_final: 0.8449 (mttp)
REVERT: B  198 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.9063 (mp)
REVERT: B  211 TYR cc_start: 0.7369 (m-80) cc_final: 0.7165 (m-80)
REVERT: B  356 ARG cc_start: 0.7945 (mmt-90) cc_final: 0.7418 (mmt-90)
REVERT: B  357 LYS cc_start: 0.9090 (mtmm) cc_final: 0.8331 (mtmt)
REVERT: B  365 GLN cc_start: 0.8637 (tp40) cc_final: 0.8221 (tp-100)
REVERT: B  368 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8177 (tm-30)
REVERT: B  382 ARG cc_start: 0.8680 (mmp80) cc_final: 0.8445 (mmp-170)
REVERT: A   47 ILE cc_start: 0.9072 (mm) cc_final: 0.8855 (mp)
REVERT: A   80 LYS cc_start: 0.8382 (mtmm) cc_final: 0.7922 (mtmm)
REVERT: A   83 ARG cc_start: 0.8036 (mmp-170) cc_final: 0.7808 (mmp-170)
REVERT: A   84 ASP cc_start: 0.8020 (m-30) cc_final: 0.7729 (m-30)
REVERT: A  198 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9048 (mp)
REVERT: A  212 ASP cc_start: 0.7789 (m-30) cc_final: 0.7406 (m-30)
REVERT: A  327 ARG cc_start: 0.7531 (ttp-170) cc_final: 0.7229 (ptt180)
REVERT: A  337 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9042 (mm)
REVERT: A  345 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8316 (mm-30)
REVERT: A  352 ASP cc_start: 0.8473 (p0) cc_final: 0.8111 (p0)
REVERT: A  357 LYS cc_start: 0.8637 (pttp) cc_final: 0.8086 (ptpp)
REVERT: A  383 GLU cc_start: 0.8613 (tm-30) cc_final: 0.7687 (tm-30)
REVERT: A  385 LEU cc_start: 0.8219 (mm) cc_final: 0.8015 (mm)
REVERT: A  387 ARG cc_start: 0.8863 (ptp-110) cc_final: 0.8550 (ptp90)
REVERT: C    3 ASP cc_start: 0.8453 (t0) cc_final: 0.8218 (t0)
REVERT: C   47 ILE cc_start: 0.9130 (mm) cc_final: 0.8814 (mp)
REVERT: C   64 HIS cc_start: 0.8465 (t-90) cc_final: 0.8116 (t-90)
REVERT: C   65 TYR cc_start: 0.6608 (m-80) cc_final: 0.6203 (m-80)
REVERT: C   84 ASP cc_start: 0.8279 (m-30) cc_final: 0.8019 (m-30)
REVERT: C  194 LYS cc_start: 0.8731 (mttm) cc_final: 0.8437 (mttm)
REVERT: C  198 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9155 (mp)
REVERT: C  281 ARG cc_start: 0.8579 (tpp-160) cc_final: 0.8287 (tpp80)
REVERT: C  308 THR cc_start: 0.7029 (m) cc_final: 0.6480 (m)
REVERT: C  355 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8465 (pm20)
REVERT: C  357 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8385 (mtmm)
REVERT: C  365 GLN cc_start: 0.8798 (tp40) cc_final: 0.8552 (tp-100)
REVERT: C  382 ARG cc_start: 0.8509 (mmp80) cc_final: 0.8049 (mmp-170)
REVERT: C  383 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8193 (tm-30)
  outliers start: 56
  outliers final: 33
  residues processed: 365
  average time/residue: 0.2629
  time to fit residues: 127.6155
Evaluate side-chains
  363 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 324
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  346 ILE
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   61 CYS
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue   31 HIS
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  161 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  323 TYR
Chi-restraints excluded: chain C residue  355 GLU
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:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 56 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
B  18 HIS
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 HIS
A 298 GLN
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 GLN
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 298 GLN
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.171186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.144863 restraints weight = 19731.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3988 rms_B_bonded: 3.85
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3984
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3984 r_free = 0.3984    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3984 r_free = 0.3984    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3984
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          1.2090

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= 0.572
  Angle     :  2.058  71.827  14404  Z= 0.910
  Chirality :  0.203   4.478   1722
  Planarity :  0.007   0.088   1632
  Dihedral  : 21.905 169.054   1932
  Min Nonbonded Distance : 1.745

Molprobity Statistics.
  All-atom Clashscore : 41.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 29.15 %
    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:  0.19 (0.25), residues: 1125
  helix:  0.75 (0.19), residues: 744
  sheet: -2.43 (0.84), residues: 30
  loop : -0.83 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 174 
 HIS   0.010   0.001   HIS B 331 
 PHE   0.037   0.003   PHE B 184 
 TYR   0.030   0.002   TYR A 211 
 ARG   0.011   0.001   ARG B 327 

*********************** 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
  392 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 343
  time to evaluate  : 1.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.6533 (m-80) cc_final: 0.6006 (m-80)
REVERT: B   80 LYS cc_start: 0.8540 (mtmm) cc_final: 0.8050 (mtmm)
REVERT: B  110 TYR cc_start: 0.7254 (m-80) cc_final: 0.6884 (m-10)
REVERT: B  173 HIS cc_start: 0.7813 (OUTLIER) cc_final: 0.7399 (m-70)
REVERT: B  180 MET cc_start: 0.8623 (mpp) cc_final: 0.8363 (mpp)
REVERT: B  194 LYS cc_start: 0.8839 (mttm) cc_final: 0.8457 (mttp)
REVERT: B  198 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.9072 (mp)
REVERT: B  211 TYR cc_start: 0.7621 (m-80) cc_final: 0.7322 (m-80)
REVERT: B  345 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7655 (mm-30)
REVERT: B  356 ARG cc_start: 0.8039 (mmt-90) cc_final: 0.7498 (mmt-90)
REVERT: B  357 LYS cc_start: 0.9007 (mtmm) cc_final: 0.8726 (mtmt)
REVERT: B  365 GLN cc_start: 0.8663 (tp40) cc_final: 0.8269 (tp-100)
REVERT: B  368 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8193 (tm-30)
REVERT: A    3 ASP cc_start: 0.8833 (t0) cc_final: 0.8632 (t0)
REVERT: A   80 LYS cc_start: 0.8379 (mtmm) cc_final: 0.7911 (mtmm)
REVERT: A   84 ASP cc_start: 0.8036 (m-30) cc_final: 0.7763 (m-30)
REVERT: A  194 LYS cc_start: 0.8971 (mttm) cc_final: 0.8353 (mttm)
REVERT: A  198 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9063 (mp)
REVERT: A  209 ASP cc_start: 0.8356 (p0) cc_final: 0.7766 (p0)
REVERT: A  212 ASP cc_start: 0.7977 (m-30) cc_final: 0.7645 (m-30)
REVERT: A  284 ASN cc_start: 0.8264 (m110) cc_final: 0.8061 (m-40)
REVERT: A  337 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9052 (mm)
REVERT: A  345 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8369 (mm-30)
REVERT: A  352 ASP cc_start: 0.8607 (p0) cc_final: 0.8399 (p0)
REVERT: A  356 ARG cc_start: 0.7985 (mmt-90) cc_final: 0.7542 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8504 (pttp) cc_final: 0.8267 (pttp)
REVERT: A  383 GLU cc_start: 0.8562 (tm-30) cc_final: 0.7655 (tm-30)
REVERT: A  385 LEU cc_start: 0.8315 (mm) cc_final: 0.8094 (mm)
REVERT: A  387 ARG cc_start: 0.8951 (ptp-110) cc_final: 0.8597 (ptp90)
REVERT: C    3 ASP cc_start: 0.8573 (t0) cc_final: 0.8314 (t0)
REVERT: C   64 HIS cc_start: 0.8559 (t-90) cc_final: 0.8235 (t-90)
REVERT: C   65 TYR cc_start: 0.6614 (m-80) cc_final: 0.6229 (m-80)
REVERT: C   84 ASP cc_start: 0.8344 (m-30) cc_final: 0.8047 (m-30)
REVERT: C  198 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9148 (mp)
REVERT: C  252 ARG cc_start: 0.8367 (mmt90) cc_final: 0.8133 (mmt90)
REVERT: C  281 ARG cc_start: 0.8559 (tpp-160) cc_final: 0.8324 (tpp80)
REVERT: C  365 GLN cc_start: 0.8832 (tp40) cc_final: 0.8540 (tp-100)
REVERT: C  383 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8184 (tm-30)
  outliers start: 49
  outliers final: 34
  residues processed: 363
  average time/residue: 0.2890
  time to fit residues: 138.4297
Evaluate side-chains
  369 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 330
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
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  343 HIS
Chi-restraints excluded: chain B residue  346 ILE
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   61 CYS
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  214 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  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   31 HIS
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  216 SER
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  257 LYS
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:    0.9980
   chunk 7 optimal weight:    7.9990
   chunk 66 optimal weight:    0.7980
   chunk 82 optimal weight:    8.9990
   chunk 15 optimal weight:    0.4980
   chunk 11 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 105 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B 163 GLN
** 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 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 217 ASN ** 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  32 GLN
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.176277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.149720 restraints weight = 19608.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.4056 rms_B_bonded: 3.88
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4051
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4051 r_free = 0.4051    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4051 r_free = 0.4051    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4051
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          1.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.191  10450  Z= 0.530
  Angle     :  2.026  71.947  14404  Z= 0.891
  Chirality :  0.197   4.331   1722
  Planarity :  0.007   0.091   1632
  Dihedral  : 22.312 169.649   1932
  Min Nonbonded Distance : 1.738

Molprobity Statistics.
  All-atom Clashscore : 40.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 31.50 %
    Favored  : 64.63 %
  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:  0.07 (0.25), residues: 1125
  helix:  0.58 (0.19), residues: 741
  sheet: -2.38 (0.85), residues: 30
  loop : -0.66 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 174 
 HIS   0.010   0.001   HIS B 331 
 PHE   0.044   0.003   PHE B 184 
 TYR   0.022   0.002   TYR A 323 
 ARG   0.013   0.002   ARG B  83 

*********************** 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
  384 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 346
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7206 (mt-10)
REVERT: B   65 TYR cc_start: 0.6437 (m-80) cc_final: 0.5922 (m-80)
REVERT: B   80 LYS cc_start: 0.8298 (mtmm) cc_final: 0.8072 (mtmm)
REVERT: B   83 ARG cc_start: 0.7998 (mmp-170) cc_final: 0.7577 (mmp-170)
REVERT: B  110 TYR cc_start: 0.7235 (m-80) cc_final: 0.6921 (m-10)
REVERT: B  173 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7428 (m-70)
REVERT: B  180 MET cc_start: 0.8627 (mpp) cc_final: 0.8140 (mpp)
REVERT: B  194 LYS cc_start: 0.8783 (mttm) cc_final: 0.8504 (mttp)
REVERT: B  198 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9060 (mp)
REVERT: B  211 TYR cc_start: 0.7545 (m-80) cc_final: 0.7265 (m-80)
REVERT: B  345 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7720 (mm-30)
REVERT: B  356 ARG cc_start: 0.7971 (mmt-90) cc_final: 0.7411 (mmt-90)
REVERT: B  357 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8693 (mtmt)
REVERT: B  368 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8157 (tm-30)
REVERT: A    3 ASP cc_start: 0.8858 (t0) cc_final: 0.8625 (t0)
REVERT: A   80 LYS cc_start: 0.8423 (mtmm) cc_final: 0.7956 (mtmm)
REVERT: A   84 ASP cc_start: 0.7979 (m-30) cc_final: 0.7719 (m-30)
REVERT: A  194 LYS cc_start: 0.9001 (mttm) cc_final: 0.8521 (mttm)
REVERT: A  212 ASP cc_start: 0.8067 (m-30) cc_final: 0.7636 (m-30)
REVERT: A  257 LYS cc_start: 0.8947 (tppp) cc_final: 0.8643 (tppt)
REVERT: A  337 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9102 (mm)
REVERT: A  345 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8419 (mm-30)
REVERT: A  356 ARG cc_start: 0.8012 (mmt-90) cc_final: 0.7457 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8461 (pttp) cc_final: 0.8131 (mtmm)
REVERT: A  383 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8139 (tm-30)
REVERT: A  387 ARG cc_start: 0.9049 (ptp-110) cc_final: 0.8726 (ptp-110)
REVERT: C    3 ASP cc_start: 0.8584 (t0) cc_final: 0.8323 (t0)
REVERT: C   47 ILE cc_start: 0.9114 (mm) cc_final: 0.8830 (mp)
REVERT: C   65 TYR cc_start: 0.6596 (m-80) cc_final: 0.6160 (m-80)
REVERT: C   69 ASP cc_start: 0.8389 (t0) cc_final: 0.8180 (t70)
REVERT: C   80 LYS cc_start: 0.8537 (mtmm) cc_final: 0.7893 (mtmm)
REVERT: C   84 ASP cc_start: 0.8370 (m-30) cc_final: 0.8064 (m-30)
REVERT: C  134 LEU cc_start: 0.9213 (mt) cc_final: 0.8590 (mt)
REVERT: C  194 LYS cc_start: 0.8836 (mttm) cc_final: 0.8436 (mttm)
REVERT: C  198 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9143 (mp)
REVERT: C  357 LYS cc_start: 0.8789 (mtmm) cc_final: 0.8551 (mtmm)
REVERT: C  365 GLN cc_start: 0.8765 (tp40) cc_final: 0.8480 (tp-100)
REVERT: C  383 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8126 (tm-30)
  outliers start: 38
  outliers final: 26
  residues processed: 365
  average time/residue: 0.2818
  time to fit residues: 134.8115
Evaluate side-chains
  359 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 329
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  346 ILE
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   61 CYS
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  230 VAL
Chi-restraints excluded: chain A residue  231 LYS
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  378 LEU
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  161 VAL
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  253 THR
Chi-restraints excluded: chain C residue  323 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 104 optimal weight:    0.6980
   chunk 110 optimal weight:    0.0980
   chunk 59 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 71 optimal weight:    5.9990
   chunk 79 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 217 ASN
** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 341 HIS
** B 380 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**
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.178526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.151635 restraints weight = 19559.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.4071 rms_B_bonded: 3.85
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4069 r_free = 0.4069    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4067 r_free = 0.4067    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4067
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          1.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.197  10450  Z= 0.533
  Angle     :  2.022  69.972  14404  Z= 0.889
  Chirality :  0.193   4.324   1722
  Planarity :  0.006   0.057   1632
  Dihedral  : 22.799 176.123   1932
  Min Nonbonded Distance : 1.712

Molprobity Statistics.
  All-atom Clashscore : 36.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 33.23 %
    Favored  : 63.20 %
  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: -0.29 (0.25), residues: 1125
  helix:  0.25 (0.18), residues: 750
  sheet: -2.02 (0.54), residues: 72
  loop : -0.47 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 174 
 HIS   0.006   0.001   HIS A 199 
 PHE   0.054   0.002   PHE C 184 
 TYR   0.021   0.002   TYR A 323 
 ARG   0.016   0.002   ARG A 382 

********************** 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
  374 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 339
  time to evaluate  : 0.984 
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   54 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7883 (mm-30)
REVERT: B   65 TYR cc_start: 0.6418 (m-80) cc_final: 0.5910 (m-80)
REVERT: B   80 LYS cc_start: 0.8191 (mtmm) cc_final: 0.7849 (mtmm)
REVERT: B  110 TYR cc_start: 0.7090 (m-80) cc_final: 0.6840 (m-10)
REVERT: B  173 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.7503 (m-70)
REVERT: B  211 TYR cc_start: 0.7494 (m-80) cc_final: 0.7167 (m-80)
REVERT: B  345 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7573 (mm-30)
REVERT: B  356 ARG cc_start: 0.7962 (mmt-90) cc_final: 0.7455 (mmt-90)
REVERT: B  357 LYS cc_start: 0.8904 (mtmm) cc_final: 0.8597 (mtmm)
REVERT: B  365 GLN cc_start: 0.8590 (tp40) cc_final: 0.8323 (tp40)
REVERT: B  368 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8072 (tm-30)
REVERT: A    2 MET cc_start: 0.8553 (ppp) cc_final: 0.8348 (ppp)
REVERT: A   80 LYS cc_start: 0.8407 (mtmm) cc_final: 0.8153 (mmmt)
REVERT: A  252 ARG cc_start: 0.8192 (mmt90) cc_final: 0.7970 (mmt90)
REVERT: A  257 LYS cc_start: 0.8961 (tppp) cc_final: 0.8645 (tppt)
REVERT: A  281 ARG cc_start: 0.7888 (tpt-90) cc_final: 0.7586 (tpp-160)
REVERT: A  337 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9029 (mm)
REVERT: A  345 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8427 (mm-30)
REVERT: A  356 ARG cc_start: 0.8045 (mmt-90) cc_final: 0.7579 (mmt-90)
REVERT: C    3 ASP cc_start: 0.8570 (t0) cc_final: 0.8359 (t0)
REVERT: C   47 ILE cc_start: 0.9164 (mm) cc_final: 0.8832 (mp)
REVERT: C   65 TYR cc_start: 0.6602 (m-80) cc_final: 0.6055 (m-80)
REVERT: C   69 ASP cc_start: 0.8314 (t0) cc_final: 0.8087 (t70)
REVERT: C   80 LYS cc_start: 0.8498 (mtmm) cc_final: 0.8030 (mtmm)
REVERT: C   84 ASP cc_start: 0.8409 (m-30) cc_final: 0.8123 (m-30)
REVERT: C  134 LEU cc_start: 0.9216 (mt) cc_final: 0.8728 (mt)
REVERT: C  149 ARG cc_start: 0.7662 (tmt170) cc_final: 0.7434 (ttt180)
REVERT: C  194 LYS cc_start: 0.8733 (mttm) cc_final: 0.8335 (mttm)
REVERT: C  198 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9189 (mp)
REVERT: C  257 LYS cc_start: 0.9113 (mmmm) cc_final: 0.8901 (mmmm)
REVERT: C  324 GLN cc_start: 0.6294 (mm-40) cc_final: 0.5587 (mm-40)
REVERT: C  357 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8401 (mtmm)
REVERT: C  365 GLN cc_start: 0.8709 (tp40) cc_final: 0.8479 (tp-100)
REVERT: C  382 ARG cc_start: 0.8572 (mmp80) cc_final: 0.8276 (mmp-170)
REVERT: C  383 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8154 (tm-30)
  outliers start: 35
  outliers final: 26
  residues processed: 354
  average time/residue: 0.2822
  time to fit residues: 132.2781
Evaluate side-chains
  346 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 317
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
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   61 CYS
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  173 HIS
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  346 ILE
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  144 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  214 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  314 LEU
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  110 TYR
Chi-restraints excluded: chain C residue  161 VAL
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  323 TYR
Chi-restraints excluded: chain C residue  378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 104 optimal weight:    5.9990
   chunk 60 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 69 optimal weight:    6.9990
   chunk 103 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 179 HIS ** 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 = 0.4385 r_free = 0.4385 target = 0.179921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.153532 restraints weight = 19368.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.4061 rms_B_bonded: 3.94
r_work (final): 0.4061
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4060 r_free = 0.4060    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 = 0.4058 r_free = 0.4058    target_work(ls_wunit_k1) = 0.149         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4058
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          1.3291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.193  10450  Z= 0.527
  Angle     :  2.018  70.592  14404  Z= 0.888
  Chirality :  0.190   4.306   1722
  Planarity :  0.006   0.058   1632
  Dihedral  : 23.002 173.793   1932
  Min Nonbonded Distance : 1.715

Molprobity Statistics.
  All-atom Clashscore : 36.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 34.35 %
    Favored  : 62.39 %
  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: -0.29 (0.25), residues: 1125
  helix:  0.36 (0.19), residues: 744
  sheet: -2.38 (0.53), residues: 72
  loop : -0.69 (0.38), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 174 
 HIS   0.008   0.001   HIS C 179 
 PHE   0.049   0.002   PHE B 184 
 TYR   0.021   0.002   TYR A 323 
 ARG   0.011   0.001   ARG A 382 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5350.68 seconds
wall clock time: 97 minutes 18.36 seconds (5838.36 seconds total)