Starting phenix.real_space_refine
on Sun Dec 29 07:41:47 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fvd_50803/12_2024/9fvd_50803.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fvd_50803/12_2024/9fvd_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_50803/12_2024/9fvd_50803.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fvd_50803/12_2024/9fvd_50803.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fvd_50803/12_2024/9fvd_50803.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fvd_50803/12_2024/9fvd_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-5532/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: 8.81, per 1000 atoms: 0.87
  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: 4.23
  Conformation dependent library (CDL) restraints added in 1.2 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: 5.83
  Creating SS restraints...
    Processing helix  chain 'B' and resid 4 through 13
      removed outlier: 4.442A  pdb=" N   LEU B  10 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   GLY B  11 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS B  13 " --> pdb=" O   LEU B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 45
    Processing helix  chain 'B' and resid 51 through 67
      removed outlier: 4.518A  pdb=" N   GLY B  55 " --> pdb=" O   ASP B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 75
    Processing helix  chain 'B' and resid 76 through 86
    Processing helix  chain 'B' and resid 99 through 104
      removed outlier: 4.292A  pdb=" N   VAL B 103 " --> pdb=" O   ARG B  99 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE B 104 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 99 through 104'
    Processing helix  chain 'B' and resid 110 through 118
    Processing helix  chain 'B' and resid 129 through 139
    Processing helix  chain 'B' and resid 148 through 165
    Processing helix  chain 'B' and resid 171 through 175
    Processing helix  chain 'B' and resid 176 through 190
    Processing helix  chain 'B' and resid 190 through 204
      removed outlier: 4.080A  pdb=" N   LYS B 194 " --> pdb=" O   SER B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 223
    Processing helix  chain 'B' and resid 227 through 237
    Processing helix  chain 'B' and resid 249 through 252
      removed outlier: 3.673A  pdb=" N   ARG B 252 " --> pdb=" O   PRO B 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 249 through 252'
    Processing helix  chain 'B' and resid 253 through 272
      removed outlier: 4.132A  pdb=" N   GLU B 259 " --> pdb=" O   LYS B 255 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ARG B 272 " --> pdb=" O   SER B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 278
      No H-bonds generated for 'chain 'B' and resid 276 through 278'
    Processing helix  chain 'B' and resid 279 through 284
    Processing helix  chain 'B' and resid 287 through 292
      removed outlier: 3.659A  pdb=" N   GLU B 292 " --> pdb=" O   ASN B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 311
    Processing helix  chain 'B' and resid 312 through 317
    Processing helix  chain 'B' and resid 323 through 350
      removed outlier: 3.782A  pdb=" N   ALA B 350 " --> pdb=" O   ILE B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 391
      removed outlier: 3.509A  pdb=" N   ARG B 356 " --> pdb=" O   ASP B 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4 through 13
      removed outlier: 4.442A  pdb=" N   LEU A  10 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   GLY A  11 " --> pdb=" O   LEU A   8 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS A  13 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 45
    Processing helix  chain 'A' and resid 51 through 67
      removed outlier: 4.519A  pdb=" N   GLY A  55 " --> pdb=" O   ASP A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 75
    Processing helix  chain 'A' and resid 76 through 86
    Processing helix  chain 'A' and resid 99 through 104
      removed outlier: 4.292A  pdb=" N   VAL A 103 " --> pdb=" O   ARG A  99 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE A 104 " --> pdb=" O   PHE A 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 99 through 104'
    Processing helix  chain 'A' and resid 110 through 118
    Processing helix  chain 'A' and resid 129 through 139
    Processing helix  chain 'A' and resid 148 through 165
    Processing helix  chain 'A' and resid 171 through 175
    Processing helix  chain 'A' and resid 176 through 190
    Processing helix  chain 'A' and resid 190 through 204
      removed outlier: 4.080A  pdb=" N   LYS A 194 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 223
    Processing helix  chain 'A' and resid 227 through 237
    Processing helix  chain 'A' and resid 249 through 252
      removed outlier: 3.673A  pdb=" N   ARG A 252 " --> pdb=" O   PRO A 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 249 through 252'
    Processing helix  chain 'A' and resid 253 through 272
      removed outlier: 4.132A  pdb=" N   GLU A 259 " --> pdb=" O   LYS A 255 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ARG A 272 " --> pdb=" O   SER A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 278
      No H-bonds generated for 'chain 'A' and resid 276 through 278'
    Processing helix  chain 'A' and resid 279 through 284
    Processing helix  chain 'A' and resid 287 through 292
      removed outlier: 3.659A  pdb=" N   GLU A 292 " --> pdb=" O   ASN A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 311
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 323 through 350
      removed outlier: 3.782A  pdb=" N   ALA A 350 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 391
      removed outlier: 3.509A  pdb=" N   ARG A 356 " --> pdb=" O   ASP A 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 13
      removed outlier: 4.441A  pdb=" N   LEU C  10 " --> pdb=" O   LEU C   7 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   GLY C  11 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS C  13 " --> pdb=" O   LEU C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 45
    Processing helix  chain 'C' and resid 51 through 67
      removed outlier: 4.518A  pdb=" N   GLY C  55 " --> pdb=" O   ASP C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 75
    Processing helix  chain 'C' and resid 76 through 86
    Processing helix  chain 'C' and resid 99 through 104
      removed outlier: 4.292A  pdb=" N   VAL C 103 " --> pdb=" O   ARG C  99 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE C 104 " --> pdb=" O   PHE C 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 99 through 104'
    Processing helix  chain 'C' and resid 110 through 118
    Processing helix  chain 'C' and resid 129 through 139
    Processing helix  chain 'C' and resid 148 through 165
    Processing helix  chain 'C' and resid 171 through 175
    Processing helix  chain 'C' and resid 176 through 190
    Processing helix  chain 'C' and resid 190 through 204
      removed outlier: 4.081A  pdb=" N   LYS C 194 " --> pdb=" O   SER C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 223
    Processing helix  chain 'C' and resid 227 through 237
    Processing helix  chain 'C' and resid 249 through 252
      removed outlier: 3.673A  pdb=" N   ARG C 252 " --> pdb=" O   PRO C 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 249 through 252'
    Processing helix  chain 'C' and resid 253 through 272
      removed outlier: 4.131A  pdb=" N   GLU C 259 " --> pdb=" O   LYS C 255 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ARG C 272 " --> pdb=" O   SER C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 276 through 278
      No H-bonds generated for 'chain 'C' and resid 276 through 278'
    Processing helix  chain 'C' and resid 279 through 284
    Processing helix  chain 'C' and resid 287 through 292
      removed outlier: 3.659A  pdb=" N   GLU C 292 " --> pdb=" O   ASN C 289 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 296 through 311
    Processing helix  chain 'C' and resid 312 through 317
    Processing helix  chain 'C' and resid 323 through 350
      removed outlier: 3.783A  pdb=" N   ALA C 350 " --> pdb=" O   ILE C 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 352 through 391
      removed outlier: 3.509A  pdb=" N   ARG C 356 " --> pdb=" O   ASP C 352 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 27
    Processing sheet with id=AA2, first strand: chain 'B' and resid 238 through 241
    Processing sheet with id=AA3, first strand: chain 'A' and resid 22 through 27
    Processing sheet with id=AA4, first strand: chain 'A' and resid 238 through 241
    Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 27
    Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 241

    609 hydrogen bonds defined for protein.
    1719 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      42 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      21 basepair parallelities
      36 stacking parallelities
  Total time for adding SS restraints: 3.58

  Time building geometry restraints manager: 4.63 seconds

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

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

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

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

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

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

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

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.33 max=1.00 mean=0.92
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     35.410
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.850
-------------------------------------------------------------------------------
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  : 1.219 
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: 0.3044
  time to fit residues: 150.4660
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  : 1.137 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
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 : 32.83
  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  : 1.064 
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: 0.6191 (m-80) cc_final: 0.5879 (m-80)
REVERT: B   80 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8195 (mtmm)
REVERT: B   88 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8105 (mm-30)
REVERT: B  198 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.9018 (mp)
REVERT: B  212 ASP cc_start: 0.8295 (m-30) cc_final: 0.7986 (m-30)
REVERT: B  345 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8118 (mm-30)
REVERT: B  357 LYS cc_start: 0.8782 (mtmm) cc_final: 0.8242 (mtmt)
REVERT: B  383 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8125 (tm-30)
REVERT: A   47 ILE cc_start: 0.9213 (mm) cc_final: 0.8936 (mp)
REVERT: A   71 ASP cc_start: 0.8148 (t0) cc_final: 0.7878 (t0)
REVERT: A   80 LYS cc_start: 0.8375 (mtmm) cc_final: 0.7923 (mtmm)
REVERT: A   81 TYR cc_start: 0.8495 (t80) cc_final: 0.8069 (t80)
REVERT: A   84 ASP cc_start: 0.8074 (m-30) cc_final: 0.7789 (m-30)
REVERT: A  198 ILE cc_start: 0.9333 (OUTLIER) cc_final: 0.8987 (mp)
REVERT: A  252 ARG cc_start: 0.8199 (mmt90) cc_final: 0.7991 (mmt90)
REVERT: A  308 THR cc_start: 0.7344 (m) cc_final: 0.6881 (m)
REVERT: A  322 GLN cc_start: 0.8938 (pm20) cc_final: 0.8687 (pm20)
REVERT: A  323 TYR cc_start: 0.8899 (m-80) cc_final: 0.8457 (m-80)
REVERT: A  324 GLN cc_start: 0.8298 (mt0) cc_final: 0.8084 (mm-40)
REVERT: A  325 GLN cc_start: 0.8505 (mp10) cc_final: 0.8272 (mp10)
REVERT: A  342 GLU cc_start: 0.8187 (pp20) cc_final: 0.7784 (pp20)
REVERT: A  345 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8058 (mm-30)
REVERT: A  356 ARG cc_start: 0.7577 (mmt-90) cc_final: 0.7242 (mmt-90)
REVERT: A  380 GLN cc_start: 0.8585 (tp-100) cc_final: 0.8349 (tp-100)
REVERT: A  383 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: C   32 GLN cc_start: 0.8727 (tp-100) cc_final: 0.8467 (tp-100)
REVERT: C  180 MET cc_start: 0.8577 (mpp) cc_final: 0.8347 (mpp)
REVERT: C  198 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9073 (mp)
REVERT: C  252 ARG cc_start: 0.8253 (mmt90) cc_final: 0.7991 (mmt90)
REVERT: C  275 GLU cc_start: 0.8173 (mp0) cc_final: 0.7970 (mp0)
REVERT: C  325 GLN cc_start: 0.8658 (mp10) cc_final: 0.8433 (mp10)
REVERT: C  345 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8084 (mm-30)
REVERT: C  356 ARG cc_start: 0.7562 (mmt-90) cc_final: 0.6996 (mmt-90)
REVERT: C  357 LYS cc_start: 0.9007 (mtmm) cc_final: 0.8450 (mtmm)
REVERT: C  380 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8369 (tp40)
REVERT: C  382 ARG cc_start: 0.8424 (mmp80) cc_final: 0.8058 (mmp-170)
REVERT: C  383 GLU cc_start: 0.8308 (tm-30) cc_final: 0.8029 (tm-30)
  outliers start: 34
  outliers final: 16
  residues processed: 395
  average time/residue: 0.3051
  time to fit residues: 157.5250
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  : 1.077 
-------------------------------------------------------------------------------
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 59 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9980
   chunk 114 optimal weight:    7.9990
   chunk 94 optimal weight:    0.9980
   chunk 105 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0980
   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 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  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: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
moved from start:          0.9245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.198  10450  Z= 0.751
  Angle     :  2.661  70.800  14404  Z= 1.190
  Chirality :  0.318   4.675   1722
  Planarity :  0.008   0.091   1632
  Dihedral  : 20.887 173.094   1932
  Min Nonbonded Distance : 1.755

Molprobity Statistics.
  All-atom Clashscore : 27.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 18.04 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.25), residues: 1125
  helix:  1.20 (0.19), residues: 720
  sheet: -2.35 (0.88), residues: 30
  loop : -1.25 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 174 
 HIS   0.006   0.001   HIS A 331 
 PHE   0.029   0.002   PHE C 184 
 TYR   0.034   0.002   TYR C 323 
 ARG   0.017   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  : 1.125 
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: 0.6429 (m-80) cc_final: 0.6106 (m-80)
REVERT: B   80 LYS cc_start: 0.8558 (mtmm) cc_final: 0.8132 (mtmm)
REVERT: B   88 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8026 (mm-30)
REVERT: B  133 PHE cc_start: 0.8679 (t80) cc_final: 0.8414 (t80)
REVERT: B  134 LEU cc_start: 0.9277 (mt) cc_final: 0.8773 (mt)
REVERT: B  148 ASP cc_start: 0.6216 (p0) cc_final: 0.5931 (p0)
REVERT: B  153 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7389 (mm-30)
REVERT: B  198 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9037 (mp)
REVERT: B  252 ARG cc_start: 0.8173 (mmt90) cc_final: 0.7934 (mmt90)
REVERT: B  259 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7729 (mm-30)
REVERT: B  308 THR cc_start: 0.7133 (m) cc_final: 0.6880 (m)
REVERT: B  323 TYR cc_start: 0.8444 (m-80) cc_final: 0.7985 (m-80)
REVERT: B  345 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8181 (mm-30)
REVERT: B  356 ARG cc_start: 0.7797 (mmt-90) cc_final: 0.7461 (mmt-90)
REVERT: B  383 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8203 (tm-30)
REVERT: A    2 MET cc_start: 0.8409 (ppp) cc_final: 0.8129 (ppp)
REVERT: A   44 ASN cc_start: 0.9047 (p0) cc_final: 0.8583 (p0)
REVERT: A   65 TYR cc_start: 0.5627 (m-80) cc_final: 0.5073 (m-80)
REVERT: A   80 LYS cc_start: 0.8351 (mtmm) cc_final: 0.7771 (mtmm)
REVERT: A   81 TYR cc_start: 0.8563 (t80) cc_final: 0.8279 (t80)
REVERT: A   84 ASP cc_start: 0.8060 (m-30) cc_final: 0.7775 (m-30)
REVERT: A  198 ILE cc_start: 0.9327 (OUTLIER) cc_final: 0.9044 (mp)
REVERT: A  200 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7529 (mm-40)
REVERT: A  252 ARG cc_start: 0.8167 (mmt90) cc_final: 0.7905 (mmt90)
REVERT: A  288 ILE cc_start: 0.8471 (tp) cc_final: 0.8083 (tp)
REVERT: A  308 THR cc_start: 0.7832 (m) cc_final: 0.6731 (m)
REVERT: A  337 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8879 (mm)
REVERT: A  345 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8098 (mm-30)
REVERT: A  354 GLU cc_start: 0.8704 (tp30) cc_final: 0.8493 (pt0)
REVERT: A  356 ARG cc_start: 0.7569 (mmt-90) cc_final: 0.7058 (mmt-90)
REVERT: A  361 GLN cc_start: 0.8799 (tp40) cc_final: 0.8542 (tm-30)
REVERT: A  365 GLN cc_start: 0.8955 (tp40) cc_final: 0.8722 (tp40)
REVERT: A  383 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8174 (tm-30)
REVERT: C   32 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8453 (tp-100)
REVERT: C   64 HIS cc_start: 0.8920 (t-90) cc_final: 0.8546 (t-90)
REVERT: C   65 TYR cc_start: 0.6288 (m-80) cc_final: 0.6011 (m-80)
REVERT: C   80 LYS cc_start: 0.8492 (mtmm) cc_final: 0.7963 (mtmm)
REVERT: C  180 MET cc_start: 0.8676 (mpp) cc_final: 0.8449 (mpp)
REVERT: C  198 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9035 (mp)
REVERT: C  234 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.8939 (mm)
REVERT: C  247 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8687 (tp)
REVERT: C  252 ARG cc_start: 0.8142 (mmt90) cc_final: 0.7857 (mmt90)
REVERT: C  275 GLU cc_start: 0.8161 (mp0) cc_final: 0.7942 (mp0)
REVERT: C  308 THR cc_start: 0.7737 (m) cc_final: 0.7488 (m)
REVERT: C  345 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8094 (mm-30)
REVERT: C  356 ARG cc_start: 0.7563 (mmt-90) cc_final: 0.6880 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8922 (mtmm) cc_final: 0.8418 (mtmm)
REVERT: C  380 GLN cc_start: 0.8621 (tp40) cc_final: 0.8408 (tp40)
REVERT: C  383 GLU cc_start: 0.8325 (tm-30) cc_final: 0.8029 (tm-30)
  outliers start: 57
  outliers final: 23
  residues processed: 422
  average time/residue: 0.2748
  time to fit residues: 153.0670
Evaluate side-chains
  381 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 352
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  228 LEU
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  313 THR
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  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 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 105 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 113 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  18 HIS
B 289 ASN
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 GLN
B 380 GLN
** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 371 HIS
C  21 ASN
C 284 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: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
moved from start:          1.0279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.205  10450  Z= 0.661
  Angle     :  2.361  70.441  14404  Z= 1.048
  Chirality :  0.303   4.627   1722
  Planarity :  0.007   0.103   1632
  Dihedral  : 21.987 171.899   1932
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 25.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 22.73 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.25), residues: 1125
  helix:  1.24 (0.19), residues: 717
  sheet: -2.60 (0.80), residues: 30
  loop : -1.21 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 174 
 HIS   0.006   0.001   HIS B 331 
 PHE   0.024   0.002   PHE C 184 
 TYR   0.030   0.002   TYR A 323 
 ARG   0.006   0.001   ARG A 327 

*********************** 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
  442 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 391
  time to evaluate  : 1.173 
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: B   65 TYR cc_start: 0.6619 (m-80) cc_final: 0.6213 (m-80)
REVERT: B   80 LYS cc_start: 0.8553 (mtmm) cc_final: 0.8307 (mtmm)
REVERT: B  148 ASP cc_start: 0.5658 (p0) cc_final: 0.5325 (p0)
REVERT: B  173 HIS cc_start: 0.7608 (t-90) cc_final: 0.7374 (t-90)
REVERT: B  194 LYS cc_start: 0.8797 (mttm) cc_final: 0.8501 (mttm)
REVERT: B  198 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9071 (mp)
REVERT: B  323 TYR cc_start: 0.7842 (m-80) cc_final: 0.7298 (m-10)
REVERT: B  332 ASP cc_start: 0.8612 (m-30) cc_final: 0.8406 (m-30)
REVERT: B  345 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8301 (mm-30)
REVERT: B  356 ARG cc_start: 0.7892 (mmt-90) cc_final: 0.7477 (mmt-90)
REVERT: B  357 LYS cc_start: 0.9022 (mtmm) cc_final: 0.8720 (mtmt)
REVERT: B  365 GLN cc_start: 0.8822 (tp40) cc_final: 0.8539 (tp-100)
REVERT: B  383 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8142 (tm-30)
REVERT: A   47 ILE cc_start: 0.9160 (mm) cc_final: 0.8903 (mp)
REVERT: A   65 TYR cc_start: 0.6017 (m-80) cc_final: 0.5367 (m-80)
REVERT: A   80 LYS cc_start: 0.8379 (mtmm) cc_final: 0.7909 (mtmm)
REVERT: A   81 TYR cc_start: 0.8558 (t80) cc_final: 0.8351 (t80)
REVERT: A   84 ASP cc_start: 0.8073 (m-30) cc_final: 0.7789 (m-30)
REVERT: A  198 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9102 (mp)
REVERT: A  209 ASP cc_start: 0.7847 (p0) cc_final: 0.7634 (p0)
REVERT: A  252 ARG cc_start: 0.8171 (mmt90) cc_final: 0.7498 (mmt90)
REVERT: A  257 LYS cc_start: 0.8992 (tppp) cc_final: 0.8433 (tppp)
REVERT: A  259 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7940 (mm-30)
REVERT: A  308 THR cc_start: 0.7915 (m) cc_final: 0.6929 (m)
REVERT: A  337 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9025 (mm)
REVERT: A  345 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8131 (mm-30)
REVERT: A  354 GLU cc_start: 0.8361 (tp30) cc_final: 0.7865 (tt0)
REVERT: A  356 ARG cc_start: 0.7679 (mmt-90) cc_final: 0.7141 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8698 (pttp) cc_final: 0.8152 (ptpp)
REVERT: A  361 GLN cc_start: 0.8835 (tp40) cc_final: 0.8597 (tm-30)
REVERT: A  368 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8199 (tm-30)
REVERT: A  383 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8175 (tm-30)
REVERT: C   32 GLN cc_start: 0.8748 (tp-100) cc_final: 0.8478 (tp-100)
REVERT: C   33 VAL cc_start: 0.8750 (m) cc_final: 0.8467 (m)
REVERT: C   47 ILE cc_start: 0.9184 (mm) cc_final: 0.8852 (mp)
REVERT: C   64 HIS cc_start: 0.8744 (t-90) cc_final: 0.8350 (t-90)
REVERT: C   65 TYR cc_start: 0.6413 (m-80) cc_final: 0.6131 (m-80)
REVERT: C  145 VAL cc_start: 0.2715 (OUTLIER) cc_final: 0.2210 (t)
REVERT: C  173 HIS cc_start: 0.7813 (t-90) cc_final: 0.7567 (t-90)
REVERT: C  198 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9131 (mp)
REVERT: C  234 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9164 (mm)
REVERT: C  252 ARG cc_start: 0.8310 (mmt90) cc_final: 0.8088 (mmt90)
REVERT: C  308 THR cc_start: 0.7503 (m) cc_final: 0.7179 (m)
REVERT: C  345 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8160 (mm-30)
REVERT: C  356 ARG cc_start: 0.7605 (mmt-90) cc_final: 0.7198 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8796 (mtmm) cc_final: 0.8320 (mtmm)
REVERT: C  365 GLN cc_start: 0.8893 (tp40) cc_final: 0.8550 (tp-100)
REVERT: C  383 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8027 (tm-30)
  outliers start: 51
  outliers final: 24
  residues processed: 417
  average time/residue: 0.2895
  time to fit residues: 157.0797
Evaluate side-chains
  371 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 341
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   78 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  268 SER
Chi-restraints excluded: chain B residue  296 TYR
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   30 ASN
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  212 ASP
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  145 VAL
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  268 SER
Chi-restraints excluded: chain C residue  314 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 84 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9990
   chunk 78 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 57 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
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**
B 380 GLN
A 200 GLN
** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 172 ASN
** C 221 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: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          1.0587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.202  10450  Z= 0.648
  Angle     :  2.278  70.549  14404  Z= 1.009
  Chirality :  0.289   4.654   1722
  Planarity :  0.007   0.128   1632
  Dihedral  : 22.097 177.714   1932
  Min Nonbonded Distance : 1.750

Molprobity Statistics.
  All-atom Clashscore : 26.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 22.94 %
    Favored  : 71.05 %
  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:  0.34 (0.25), residues: 1125
  helix:  1.04 (0.19), residues: 720
  sheet: -2.43 (0.85), residues: 30
  loop : -1.07 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 174 
 HIS   0.008   0.001   HIS A 331 
 PHE   0.034   0.002   PHE B 184 
 TYR   0.016   0.002   TYR A 211 
 ARG   0.013   0.001   ARG B 339 

*********************** 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
  432 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 373
  time to evaluate  : 1.050 
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: 0.6550 (m-80) cc_final: 0.6033 (m-80)
REVERT: B  110 TYR cc_start: 0.7329 (m-80) cc_final: 0.6959 (m-10)
REVERT: B  173 HIS cc_start: 0.7694 (t-90) cc_final: 0.7457 (t-90)
REVERT: B  198 ILE cc_start: 0.9393 (OUTLIER) cc_final: 0.9102 (mp)
REVERT: B  276 TYR cc_start: 0.8967 (m-80) cc_final: 0.8691 (m-80)
REVERT: B  357 LYS cc_start: 0.9083 (mtmm) cc_final: 0.8728 (mtmm)
REVERT: B  365 GLN cc_start: 0.8851 (tp40) cc_final: 0.8360 (tp-100)
REVERT: B  368 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8213 (tm-30)
REVERT: B  383 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8120 (tm-30)
REVERT: A   64 HIS cc_start: 0.8865 (t-90) cc_final: 0.8644 (t70)
REVERT: A   80 LYS cc_start: 0.8342 (mtmm) cc_final: 0.7849 (mtmm)
REVERT: A   81 TYR cc_start: 0.8511 (t80) cc_final: 0.8300 (t80)
REVERT: A   83 ARG cc_start: 0.8159 (mmp-170) cc_final: 0.7908 (mmp-170)
REVERT: A   84 ASP cc_start: 0.8173 (m-30) cc_final: 0.7881 (m-30)
REVERT: A   87 TYR cc_start: 0.8746 (m-80) cc_final: 0.7638 (m-80)
REVERT: A   88 GLU cc_start: 0.8237 (tp30) cc_final: 0.7954 (tp30)
REVERT: A  194 LYS cc_start: 0.8870 (mttm) cc_final: 0.8555 (mtmm)
REVERT: A  198 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9067 (mp)
REVERT: A  252 ARG cc_start: 0.8333 (mmt90) cc_final: 0.8046 (mmt90)
REVERT: A  337 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8971 (mm)
REVERT: A  345 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8177 (mm-30)
REVERT: A  354 GLU cc_start: 0.8429 (tp30) cc_final: 0.7826 (tt0)
REVERT: A  356 ARG cc_start: 0.7824 (mmt-90) cc_final: 0.7363 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8707 (pttp) cc_final: 0.8176 (ptpp)
REVERT: A  361 GLN cc_start: 0.8857 (tp40) cc_final: 0.8581 (tm-30)
REVERT: A  383 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8312 (tm-30)
REVERT: C    3 ASP cc_start: 0.8519 (t0) cc_final: 0.8285 (t0)
REVERT: C   33 VAL cc_start: 0.8720 (m) cc_final: 0.8464 (m)
REVERT: C   64 HIS cc_start: 0.8916 (t-90) cc_final: 0.8705 (t-90)
REVERT: C   65 TYR cc_start: 0.6593 (m-80) cc_final: 0.6289 (m-80)
REVERT: C   84 ASP cc_start: 0.8112 (m-30) cc_final: 0.7824 (m-30)
REVERT: C   87 TYR cc_start: 0.8854 (m-80) cc_final: 0.8578 (m-80)
REVERT: C  198 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9116 (mp)
REVERT: C  234 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9147 (mm)
REVERT: C  252 ARG cc_start: 0.8362 (mmt90) cc_final: 0.8028 (mmt90)
REVERT: C  356 ARG cc_start: 0.7722 (mmt-90) cc_final: 0.7182 (mmt-90)
REVERT: C  365 GLN cc_start: 0.8914 (tp40) cc_final: 0.8531 (tp-100)
REVERT: C  383 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8039 (tm-30)
  outliers start: 59
  outliers final: 35
  residues processed: 398
  average time/residue: 0.2867
  time to fit residues: 149.1535
Evaluate side-chains
  365 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 325
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
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  104 ILE
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  343 HIS
Chi-restraints excluded: chain B residue  361 GLN
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain A residue   31 HIS
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue   59 THR
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  200 GLN
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  374 THR
Chi-restraints excluded: chain C residue   23 LYS
Chi-restraints excluded: chain C residue   30 ASN
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  212 ASP
Chi-restraints excluded: chain C residue  216 SER
Chi-restraints excluded: chain C residue  234 LEU
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  257 LYS
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  354 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 113 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 109 optimal weight:   10.0000
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  74 ASN
B 217 ASN
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 GLN
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 200 GLN
A 293 HIS
A 318 ASN
** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 ASN
** C 158 GLN ** 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: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          1.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.196  10450  Z= 0.591
  Angle     :  2.157  71.153  14404  Z= 0.949
  Chirality :  0.256   4.534   1722
  Planarity :  0.007   0.081   1632
  Dihedral  : 21.655 167.742   1932
  Min Nonbonded Distance : 1.742

Molprobity Statistics.
  All-atom Clashscore : 26.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 26.91 %
    Favored  : 67.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.25), residues: 1125
  helix:  0.85 (0.19), residues: 729
  sheet: -2.57 (0.79), residues: 30
  loop : -0.86 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 174 
 HIS   0.008   0.001   HIS A 331 
 PHE   0.031   0.002   PHE A 184 
 TYR   0.021   0.002   TYR C 211 
 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
  405 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 355
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 ILE cc_start: 0.9066 (mm) cc_final: 0.8860 (mp)
REVERT: B   65 TYR cc_start: 0.6609 (m-80) cc_final: 0.6019 (m-80)
REVERT: B   80 LYS cc_start: 0.8605 (mtmm) cc_final: 0.8318 (mtmm)
REVERT: B   81 TYR cc_start: 0.8348 (t80) cc_final: 0.8129 (t80)
REVERT: B  110 TYR cc_start: 0.7372 (m-80) cc_final: 0.7055 (m-10)
REVERT: B  134 LEU cc_start: 0.9069 (mt) cc_final: 0.8412 (mt)
REVERT: B  173 HIS cc_start: 0.7680 (t-90) cc_final: 0.7414 (t-90)
REVERT: B  180 MET cc_start: 0.8839 (mpp) cc_final: 0.8582 (mpp)
REVERT: B  198 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9028 (mp)
REVERT: B  257 LYS cc_start: 0.8890 (tppp) cc_final: 0.8684 (mmtp)
REVERT: B  259 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7736 (mm-30)
REVERT: B  334 GLU cc_start: 0.8551 (tp30) cc_final: 0.8294 (tp30)
REVERT: B  345 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7779 (mm-30)
REVERT: B  357 LYS cc_start: 0.9046 (mtmm) cc_final: 0.8456 (mtmt)
REVERT: B  365 GLN cc_start: 0.8766 (tp40) cc_final: 0.8456 (tp-100)
REVERT: B  383 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8050 (tm-30)
REVERT: A   47 ILE cc_start: 0.9127 (mm) cc_final: 0.8909 (mp)
REVERT: A   80 LYS cc_start: 0.8375 (mtmm) cc_final: 0.7873 (mtmm)
REVERT: A   81 TYR cc_start: 0.8457 (t80) cc_final: 0.8228 (t80)
REVERT: A   84 ASP cc_start: 0.8118 (m-30) cc_final: 0.7817 (m-30)
REVERT: A   93 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8827 (mmmm)
REVERT: A  198 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.9053 (mp)
REVERT: A  251 VAL cc_start: 0.9155 (m) cc_final: 0.8943 (m)
REVERT: A  257 LYS cc_start: 0.8976 (tppp) cc_final: 0.8696 (tppt)
REVERT: A  259 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8190 (mm-30)
REVERT: A  337 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9042 (mm)
REVERT: A  345 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8182 (mm-30)
REVERT: A  354 GLU cc_start: 0.8466 (tp30) cc_final: 0.7927 (tt0)
REVERT: A  357 LYS cc_start: 0.8627 (pttp) cc_final: 0.8082 (ptpp)
REVERT: A  368 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: A  383 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8034 (tm-30)
REVERT: A  387 ARG cc_start: 0.8892 (ptp-110) cc_final: 0.8218 (ptp90)
REVERT: C    3 ASP cc_start: 0.8581 (t0) cc_final: 0.8279 (t0)
REVERT: C   32 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8454 (tp-100)
REVERT: C   47 ILE cc_start: 0.9142 (mm) cc_final: 0.8833 (mp)
REVERT: C   64 HIS cc_start: 0.8710 (t-90) cc_final: 0.8258 (t-90)
REVERT: C   65 TYR cc_start: 0.6613 (m-80) cc_final: 0.6092 (m-80)
REVERT: C   80 LYS cc_start: 0.8552 (mtmm) cc_final: 0.8059 (mtmm)
REVERT: C   84 ASP cc_start: 0.8033 (m-30) cc_final: 0.7750 (m-30)
REVERT: C   87 TYR cc_start: 0.8813 (m-80) cc_final: 0.8578 (m-80)
REVERT: C  194 LYS cc_start: 0.8642 (mttm) cc_final: 0.8383 (mttm)
REVERT: C  198 ILE cc_start: 0.9374 (OUTLIER) cc_final: 0.9103 (mp)
REVERT: C  281 ARG cc_start: 0.8568 (tpp80) cc_final: 0.8321 (tpp80)
REVERT: C  324 GLN cc_start: 0.6179 (mm-40) cc_final: 0.5788 (mm-40)
REVERT: C  356 ARG cc_start: 0.7603 (mmt-90) cc_final: 0.7114 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8880 (mtpp) cc_final: 0.8619 (mtmm)
REVERT: C  365 GLN cc_start: 0.8903 (tp40) cc_final: 0.8514 (tp-100)
REVERT: C  382 ARG cc_start: 0.8356 (mmp80) cc_final: 0.8093 (mmp-170)
REVERT: C  383 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8138 (tm-30)
  outliers start: 50
  outliers final: 28
  residues processed: 375
  average time/residue: 0.2911
  time to fit residues: 143.4367
Evaluate side-chains
  366 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 334
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   48 ASP
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  200 GLN
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  378 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  197 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  216 SER
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  323 TYR
Chi-restraints excluded: chain C residue  354 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 82 optimal weight:    9.9990
   chunk 95 optimal weight:    4.9990
   chunk 63 optimal weight:    0.8980
   chunk 112 optimal weight:    5.9990
   chunk 70 optimal weight:    7.9990
   chunk 68 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 69 optimal weight:    0.3980
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 GLN
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 298 GLN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 179 HIS
C 338 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
moved from start:          1.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.195  10450  Z= 0.592
  Angle     :  2.180  71.768  14404  Z= 0.948
  Chirality :  0.229   4.380   1722
  Planarity :  0.007   0.086   1632
  Dihedral  : 21.435 163.379   1932
  Min Nonbonded Distance : 1.749

Molprobity Statistics.
  All-atom Clashscore : 26.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 25.79 %
    Favored  : 68.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.25), residues: 1125
  helix:  0.68 (0.19), residues: 750
  sheet: -1.75 (0.54), residues: 72
  loop : -0.71 (0.38), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 174 
 HIS   0.006   0.001   HIS A 331 
 PHE   0.038   0.003   PHE C 184 
 TYR   0.020   0.002   TYR C 211 
 ARG   0.011   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
  397 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 341
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.6503 (m-80) cc_final: 0.5919 (m-80)
REVERT: B   80 LYS cc_start: 0.8587 (mtmm) cc_final: 0.8323 (mtmm)
REVERT: B  110 TYR cc_start: 0.7367 (m-80) cc_final: 0.7004 (m-10)
REVERT: B  118 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8582 (ptpt)
REVERT: B  134 LEU cc_start: 0.9090 (mt) cc_final: 0.8436 (mt)
REVERT: B  148 ASP cc_start: 0.5978 (p0) cc_final: 0.5561 (p0)
REVERT: B  173 HIS cc_start: 0.7585 (t-90) cc_final: 0.7374 (t-90)
REVERT: B  180 MET cc_start: 0.8739 (mpp) cc_final: 0.8276 (mpp)
REVERT: B  198 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9093 (mp)
REVERT: B  204 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7766 (tt)
REVERT: B  257 LYS cc_start: 0.9020 (tppp) cc_final: 0.8766 (mmtp)
REVERT: B  259 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7914 (mm-30)
REVERT: B  334 GLU cc_start: 0.8587 (tp30) cc_final: 0.8206 (tp30)
REVERT: B  338 GLN cc_start: 0.8495 (mm-40) cc_final: 0.7974 (mm-40)
REVERT: B  345 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7607 (mm-30)
REVERT: B  357 LYS cc_start: 0.9054 (mtmm) cc_final: 0.8742 (mtmm)
REVERT: B  365 GLN cc_start: 0.8772 (tp40) cc_final: 0.8488 (tp-100)
REVERT: B  383 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8026 (tm-30)
REVERT: A    3 ASP cc_start: 0.8735 (t0) cc_final: 0.8510 (t0)
REVERT: A   47 ILE cc_start: 0.9159 (mm) cc_final: 0.8923 (mp)
REVERT: A   80 LYS cc_start: 0.8367 (mtmm) cc_final: 0.7829 (mtmm)
REVERT: A   83 ARG cc_start: 0.8186 (mmp-170) cc_final: 0.7979 (mmp-170)
REVERT: A   84 ASP cc_start: 0.8171 (m-30) cc_final: 0.7882 (m-30)
REVERT: A   93 LYS cc_start: 0.9060 (mmmm) cc_final: 0.8852 (mmmm)
REVERT: A  194 LYS cc_start: 0.8971 (mttm) cc_final: 0.8361 (mttm)
REVERT: A  198 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9057 (mp)
REVERT: A  337 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9046 (mm)
REVERT: A  345 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8258 (mm-30)
REVERT: A  354 GLU cc_start: 0.8584 (tp30) cc_final: 0.7870 (tt0)
REVERT: A  357 LYS cc_start: 0.8675 (pttp) cc_final: 0.8193 (ptpp)
REVERT: A  383 GLU cc_start: 0.8462 (tm-30) cc_final: 0.7847 (tm-30)
REVERT: A  385 LEU cc_start: 0.8223 (mm) cc_final: 0.7958 (mm)
REVERT: A  387 ARG cc_start: 0.8905 (ptp-110) cc_final: 0.8213 (ptp90)
REVERT: C    3 ASP cc_start: 0.8606 (t0) cc_final: 0.8374 (t0)
REVERT: C   47 ILE cc_start: 0.9174 (mm) cc_final: 0.8829 (mp)
REVERT: C   65 TYR cc_start: 0.6680 (m-80) cc_final: 0.6214 (m-80)
REVERT: C   80 LYS cc_start: 0.8592 (mtmm) cc_final: 0.7882 (mtmm)
REVERT: C   84 ASP cc_start: 0.8116 (m-30) cc_final: 0.7817 (m-30)
REVERT: C   87 TYR cc_start: 0.8840 (m-80) cc_final: 0.7658 (m-80)
REVERT: C  198 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9138 (mp)
REVERT: C  252 ARG cc_start: 0.8420 (mmt90) cc_final: 0.8185 (mmt90)
REVERT: C  281 ARG cc_start: 0.8566 (tpp80) cc_final: 0.8263 (tpp80)
REVERT: C  356 ARG cc_start: 0.7685 (mmt-90) cc_final: 0.7247 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8938 (mtpp) cc_final: 0.8666 (mtmm)
REVERT: C  365 GLN cc_start: 0.8927 (tp40) cc_final: 0.8597 (tp-100)
REVERT: C  383 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8079 (tm-30)
  outliers start: 56
  outliers final: 37
  residues processed: 367
  average time/residue: 0.2847
  time to fit residues: 136.8270
Evaluate side-chains
  359 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 317
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
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  198 ILE
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  255 LYS
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  354 GLU
Chi-restraints excluded: chain B residue  374 THR
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  144 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  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  103 VAL
Chi-restraints excluded: chain C residue  104 ILE
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  161 VAL
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  212 ASP
Chi-restraints excluded: chain C residue  216 SER
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  257 LYS
Chi-restraints excluded: chain C residue  268 SER
Chi-restraints excluded: chain C residue  354 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 67 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 22 optimal weight:    0.4980
   chunk 21 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9980
   chunk 10 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B  74 ASN
** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 200 GLN
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
moved from start:          1.2391

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= 0.559
  Angle     :  2.114  70.875  14404  Z= 0.916
  Chirality :  0.230   4.495   1722
  Planarity :  0.006   0.062   1632
  Dihedral  : 21.714 164.282   1932
  Min Nonbonded Distance : 1.725

Molprobity Statistics.
  All-atom Clashscore : 25.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 28.03 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.25), residues: 1125
  helix:  0.56 (0.19), residues: 750
  sheet: -1.83 (0.55), residues: 72
  loop : -0.76 (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 B 331 
 PHE   0.043   0.002   PHE C 184 
 TYR   0.020   0.002   TYR A 323 
 ARG   0.013   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
  421 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 375
  time to evaluate  : 1.129 
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    9 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7141 (mt-10)
REVERT: B   65 TYR cc_start: 0.6490 (m-80) cc_final: 0.5914 (m-80)
REVERT: B   80 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8190 (mtmm)
REVERT: B  110 TYR cc_start: 0.7396 (m-80) cc_final: 0.7070 (m-10)
REVERT: B  134 LEU cc_start: 0.8969 (mt) cc_final: 0.8242 (mt)
REVERT: B  148 ASP cc_start: 0.5803 (p0) cc_final: 0.5445 (p0)
REVERT: B  180 MET cc_start: 0.8757 (mpp) cc_final: 0.8118 (mpp)
REVERT: B  181 LYS cc_start: 0.9019 (mmmt) cc_final: 0.8726 (tptt)
REVERT: B  198 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9050 (mp)
REVERT: B  209 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7604 (p0)
REVERT: B  276 TYR cc_start: 0.8957 (m-80) cc_final: 0.8726 (m-80)
REVERT: B  338 GLN cc_start: 0.8529 (mm-40) cc_final: 0.8058 (mm-40)
REVERT: B  345 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7509 (mm-30)
REVERT: B  357 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8605 (mtmm)
REVERT: B  365 GLN cc_start: 0.8706 (tp40) cc_final: 0.8490 (tp-100)
REVERT: A   47 ILE cc_start: 0.9126 (mm) cc_final: 0.8925 (mp)
REVERT: A   80 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7839 (mtmm)
REVERT: A   84 ASP cc_start: 0.8153 (m-30) cc_final: 0.7869 (m-30)
REVERT: A   87 TYR cc_start: 0.8480 (m-80) cc_final: 0.7521 (m-80)
REVERT: A  198 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.9058 (mp)
REVERT: A  337 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9025 (mm)
REVERT: A  345 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8210 (mm-30)
REVERT: A  354 GLU cc_start: 0.8448 (tp30) cc_final: 0.7887 (tt0)
REVERT: A  356 ARG cc_start: 0.7972 (mmt-90) cc_final: 0.7478 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8643 (pttp) cc_final: 0.8138 (ptpp)
REVERT: C    3 ASP cc_start: 0.8628 (t0) cc_final: 0.8390 (t0)
REVERT: C   27 PHE cc_start: 0.6348 (m-10) cc_final: 0.6046 (m-80)
REVERT: C   32 GLN cc_start: 0.8868 (tp-100) cc_final: 0.8578 (tp-100)
REVERT: C   47 ILE cc_start: 0.9089 (mm) cc_final: 0.8796 (mp)
REVERT: C   65 TYR cc_start: 0.6664 (m-80) cc_final: 0.6129 (m-80)
REVERT: C   84 ASP cc_start: 0.8093 (m-30) cc_final: 0.7815 (m-30)
REVERT: C  194 LYS cc_start: 0.8584 (mttm) cc_final: 0.8299 (mttm)
REVERT: C  198 ILE cc_start: 0.9392 (OUTLIER) cc_final: 0.9109 (mp)
REVERT: C  211 TYR cc_start: 0.6595 (m-80) cc_final: 0.6354 (m-80)
REVERT: C  252 ARG cc_start: 0.8358 (mmt90) cc_final: 0.8047 (mmt90)
REVERT: C  356 ARG cc_start: 0.7607 (mmt-90) cc_final: 0.7105 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8576 (mtmm)
REVERT: C  365 GLN cc_start: 0.8866 (tp40) cc_final: 0.8551 (tp-100)
REVERT: C  382 ARG cc_start: 0.8410 (mmp80) cc_final: 0.8132 (mmp-170)
REVERT: C  383 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8082 (tm-30)
  outliers start: 46
  outliers final: 26
  residues processed: 395
  average time/residue: 0.2961
  time to fit residues: 151.9229
Evaluate side-chains
  364 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 333
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
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  198 ILE
Chi-restraints excluded: chain B residue  209 ASP
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain A residue    9 GLU
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  198 ILE
Chi-restraints excluded: chain A residue  200 GLN
Chi-restraints excluded: chain A residue  214 ILE
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 C residue   23 LYS
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  216 SER
Chi-restraints excluded: chain C residue  253 THR
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 98 optimal weight:    0.9980
   chunk 105 optimal weight:    0.5980
   chunk 108 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   chunk 45 optimal weight:    0.3980
   chunk 82 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9990
   chunk 94 optimal weight:    0.8980
   chunk 99 optimal weight:   10.0000
   chunk 104 optimal weight:    0.6980
   chunk 69 optimal weight:    0.0980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 298 GLN
** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 GLN
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 298 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6860
moved from start:          1.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.193  10450  Z= 0.565
  Angle     :  2.093  69.957  14404  Z= 0.909
  Chirality :  0.228   4.443   1722
  Planarity :  0.006   0.057   1632
  Dihedral  : 21.831 164.632   1932
  Min Nonbonded Distance : 1.709

Molprobity Statistics.
  All-atom Clashscore : 24.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 28.13 %
    Favored  : 67.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.25), residues: 1125
  helix:  0.45 (0.19), residues: 756
  sheet: -2.18 (0.52), residues: 72
  loop : -0.76 (0.39), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 174 
 HIS   0.006   0.001   HIS A 199 
 PHE   0.049   0.002   PHE C 184 
 TYR   0.020   0.002   TYR A 323 
 ARG   0.015   0.001   ARG A 382 

*********************** 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
  383 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 342
  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: B    9 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7119 (mt-10)
REVERT: B   65 TYR cc_start: 0.6605 (m-80) cc_final: 0.5925 (m-80)
REVERT: B   71 ASP cc_start: 0.7762 (t0) cc_final: 0.7527 (t0)
REVERT: B   80 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8184 (mtmm)
REVERT: B   81 TYR cc_start: 0.8076 (t80) cc_final: 0.7810 (t80)
REVERT: B  110 TYR cc_start: 0.7282 (m-80) cc_final: 0.6965 (m-10)
REVERT: B  134 LEU cc_start: 0.8779 (mt) cc_final: 0.8111 (mt)
REVERT: B  180 MET cc_start: 0.8711 (mpp) cc_final: 0.8089 (mpp)
REVERT: B  194 LYS cc_start: 0.8348 (mttp) cc_final: 0.7686 (mmtp)
REVERT: B  198 ILE cc_start: 0.9379 (OUTLIER) cc_final: 0.9087 (mp)
REVERT: B  257 LYS cc_start: 0.8947 (tppp) cc_final: 0.8697 (mmtp)
REVERT: B  276 TYR cc_start: 0.8880 (m-80) cc_final: 0.8659 (m-80)
REVERT: B  345 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7481 (mm-30)
REVERT: B  357 LYS cc_start: 0.8894 (mtmm) cc_final: 0.8516 (mtmm)
REVERT: A   80 LYS cc_start: 0.8320 (mtmm) cc_final: 0.7872 (mtmm)
REVERT: A   88 GLU cc_start: 0.8015 (tp30) cc_final: 0.7807 (tp30)
REVERT: A  194 LYS cc_start: 0.8759 (mttm) cc_final: 0.8204 (mttm)
REVERT: A  198 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.9001 (mp)
REVERT: A  257 LYS cc_start: 0.8919 (tppp) cc_final: 0.8634 (tppt)
REVERT: A  337 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9111 (mm)
REVERT: A  354 GLU cc_start: 0.8407 (tp30) cc_final: 0.7882 (tt0)
REVERT: A  357 LYS cc_start: 0.8651 (pttp) cc_final: 0.8123 (ptpp)
REVERT: C    3 ASP cc_start: 0.8601 (t0) cc_final: 0.8319 (t0)
REVERT: C   47 ILE cc_start: 0.9034 (mm) cc_final: 0.8817 (mp)
REVERT: C   65 TYR cc_start: 0.6735 (m-80) cc_final: 0.6170 (m-80)
REVERT: C   80 LYS cc_start: 0.8550 (mtmm) cc_final: 0.8015 (mtmm)
REVERT: C   84 ASP cc_start: 0.8099 (m-30) cc_final: 0.7803 (m-30)
REVERT: C  198 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9124 (mp)
REVERT: C  257 LYS cc_start: 0.9126 (mmmm) cc_final: 0.8914 (mmmm)
REVERT: C  365 GLN cc_start: 0.8811 (tp40) cc_final: 0.8542 (tp-100)
REVERT: C  383 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8044 (tm-30)
  outliers start: 41
  outliers final: 30
  residues processed: 363
  average time/residue: 0.2576
  time to fit residues: 125.5256
Evaluate side-chains
  350 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 316
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   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  198 ILE
Chi-restraints excluded: chain A residue  214 ILE
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 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  319 VAL
Chi-restraints excluded: chain C residue  378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 77 optimal weight:    0.5980
   chunk 116 optimal weight:    5.9990
   chunk 107 optimal weight:    0.6980
   chunk 92 optimal weight:    0.0570
   chunk 9 optimal weight:    0.0070
   chunk 71 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 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 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 ASN
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 293 HIS
** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6815
moved from start:          1.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.200  10450  Z= 0.560
  Angle     :  2.062  68.607  14404  Z= 0.896
  Chirality :  0.225   4.473   1722
  Planarity :  0.006   0.061   1632
  Dihedral  : 22.048 166.595   1932
  Min Nonbonded Distance : 1.692

Molprobity Statistics.
  All-atom Clashscore : 23.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 31.70 %
    Favored  : 65.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.25), residues: 1125
  helix:  0.37 (0.19), residues: 747
  sheet: -2.56 (0.51), residues: 72
  loop : -0.74 (0.39), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 174 
 HIS   0.009   0.001   HIS B 310 
 PHE   0.030   0.002   PHE C 184 
 TYR   0.019   0.001   TYR A 323 
 ARG   0.011   0.001   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
  359 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 329
  time to evaluate  : 1.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    3 ASP cc_start: 0.8680 (t0) cc_final: 0.8445 (t0)
REVERT: B    9 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6987 (mt-10)
REVERT: B   65 TYR cc_start: 0.6627 (m-80) cc_final: 0.5951 (m-80)
REVERT: B   80 LYS cc_start: 0.8434 (mtmm) cc_final: 0.7962 (mtmm)
REVERT: B  134 LEU cc_start: 0.8761 (mt) cc_final: 0.8120 (mt)
REVERT: B  180 MET cc_start: 0.8552 (mpp) cc_final: 0.8070 (mpp)
REVERT: B  194 LYS cc_start: 0.8404 (mttp) cc_final: 0.7772 (mmtp)
REVERT: B  198 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9105 (mp)
REVERT: B  257 LYS cc_start: 0.8941 (tppp) cc_final: 0.8644 (mmmm)
REVERT: B  345 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7498 (mm-30)
REVERT: B  356 ARG cc_start: 0.7920 (mmt-90) cc_final: 0.7408 (mmt-90)
REVERT: B  357 LYS cc_start: 0.8769 (mtmm) cc_final: 0.8451 (mtmm)
REVERT: B  365 GLN cc_start: 0.8349 (tp40) cc_final: 0.8106 (tp-100)
REVERT: A   88 GLU cc_start: 0.7951 (tp30) cc_final: 0.7594 (tp30)
REVERT: A  159 VAL cc_start: 0.8642 (t) cc_final: 0.8428 (m)
REVERT: A  257 LYS cc_start: 0.8837 (tppp) cc_final: 0.8575 (tppt)
REVERT: A  337 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9143 (mm)
REVERT: A  354 GLU cc_start: 0.8344 (tp30) cc_final: 0.7890 (tt0)
REVERT: A  356 ARG cc_start: 0.7986 (mmt-90) cc_final: 0.7578 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8636 (pttp) cc_final: 0.8101 (ptpp)
REVERT: C    3 ASP cc_start: 0.8616 (t0) cc_final: 0.8386 (t0)
REVERT: C   65 TYR cc_start: 0.6714 (m-80) cc_final: 0.6174 (m-80)
REVERT: C   80 LYS cc_start: 0.8523 (mtmm) cc_final: 0.7977 (mtmm)
REVERT: C   84 ASP cc_start: 0.8116 (m-30) cc_final: 0.7840 (m-30)
REVERT: C  198 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9145 (mp)
REVERT: C  324 GLN cc_start: 0.5403 (mm-40) cc_final: 0.5114 (mm-40)
REVERT: C  357 LYS cc_start: 0.8642 (mtpp) cc_final: 0.8385 (ptpp)
REVERT: C  365 GLN cc_start: 0.8744 (tp40) cc_final: 0.8491 (tp-100)
REVERT: C  383 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8180 (tm-30)
  outliers start: 30
  outliers final: 22
  residues processed: 341
  average time/residue: 0.2950
  time to fit residues: 133.6930
Evaluate side-chains
  329 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 304
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   61 CYS
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain A residue   23 LYS
Chi-restraints excluded: chain A residue   30 ASN
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  214 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain C residue   23 LYS
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  103 VAL
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain C residue  161 VAL
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  319 VAL
Chi-restraints excluded: chain C residue  378 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 85 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 92 optimal weight:    0.4980
   chunk 38 optimal weight:    0.0470
   chunk 95 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.6480

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

Flipped N/Q/H residues before XYZ refinement:
B 217 ASN
** B 221 GLN ** 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 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 380 GLN
C  74 ASN
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 318 ASN ** 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 = 0.4430 r_free = 0.4430 target = 0.187288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.161849 restraints weight = 19367.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.4154 rms_B_bonded: 4.00
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4149 r_free = 0.4149    target_work(ls_wunit_k1) = 0.161         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4135 r_free = 0.4135    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
moved from start:          1.3958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.201  10450  Z= 0.553
  Angle     :  2.033  68.537  14404  Z= 0.883
  Chirality :  0.217   4.434   1722
  Planarity :  0.006   0.076   1632
  Dihedral  : 22.020 171.617   1932
  Min Nonbonded Distance : 1.691

Molprobity Statistics.
  All-atom Clashscore : 29.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 32.42 %
    Favored  : 64.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (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: -0.15 (0.25), residues: 1125
  helix:  0.47 (0.19), residues: 753
  sheet: -2.71 (0.52), residues: 72
  loop : -0.56 (0.40), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 174 
 HIS   0.009   0.001   HIS A 199 
 PHE   0.016   0.002   PHE C 184 
 TYR   0.018   0.002   TYR A 323 
 ARG   0.011   0.001   ARG B 387 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3351.80 seconds
wall clock time: 62 minutes 15.49 seconds (3735.49 seconds total)