Starting phenix.real_space_refine
on Thu Jul  2 20:16:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fvd_50803/07_2026/9fvd_50803.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fvd_50803/07_2026/9fvd_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_50803/07_2026/9fvd_50803.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fvd_50803/07_2026/9fvd_50803.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fvd_50803/07_2026/9fvd_50803.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fvd_50803/07_2026/9fvd_50803.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      54      5.49       5
     S      15      5.16       5
     C    6240      2.51       5
     N    1833      2.21       5
     O    2004      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10146
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2991
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 2991
          Classifications: {'peptide': 381}
          Link IDs: {'PTRANS': 10, 'TRANS': 370}
          Chain breaks: 2
    Chain: "S"
      Number of atoms: 391
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 391
          Classifications: {'RNA': 18}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 11, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 3, 'rna3p': 14}
    Chain: "R"
      Number of atoms: 261
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 261
          Classifications: {'RNA': 12}
          Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 2, 'rna3p': 9}
    Chain: "Q"
      Number of atoms: 130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 130
          Classifications: {'RNA': 6}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 1, 'rna3p': 4}
    Chain: "U"
      Number of atoms: 260
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 260
          Classifications: {'RNA': 12}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 7, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 2, 'rna3p': 9}
    Chain: "T"
      Number of atoms: 131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 131
          Classifications: {'RNA': 6}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1}
          Link IDs: {'rna2p': 1, 'rna3p': 4}
  Restraints were copied for chains:
    B, C
  Residues with excluded nonbonded symmetry interactions: 54
    residue:
      pdb=" P     A S   1 " occ=0.33
      ... (21 atoms not shown)
      pdb=" OP3   A S   1 " occ=0.33
    residue:
      pdb=" P     G S   2 " occ=0.33
      ... (21 atoms not shown)
      pdb=" C4    G S   2 " occ=0.33
    residue:
      pdb=" P     A S   3 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S   3 " occ=0.33
    residue:
      pdb=" P     C S   4 " occ=0.33
      ... (18 atoms not shown)
      pdb=" C6    C S   4 " occ=0.33
    residue:
      pdb=" P     A S   5 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S   5 " occ=0.33
    residue:
      pdb=" P     C S   6 " occ=0.33
      ... (18 atoms not shown)
      pdb=" C6    C S   6 " occ=0.33
    residue:
      pdb=" P     A S   7 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S   7 " occ=0.33
    residue:
      pdb=" P     C S   8 " occ=0.33
      ... (18 atoms not shown)
      pdb=" C6    C S   8 " occ=0.33
    residue:
      pdb=" P     A S   9 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S   9 " occ=0.33
    residue:
      pdb=" P     A S  10 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S  10 " occ=0.33
    residue:
      pdb=" P     A S  11 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S  11 " occ=0.33
    residue:
      pdb=" P     A S  12 " occ=0.33
      ... (20 atoms not shown)
      pdb=" C4    A S  12 " occ=0.33
    ... (remaining 42 not shown)
  Time building chain proxies: 1.82, per 1000 atoms: 0.18
  Number of scatterers: 10146
  At special positions: 0
  Unit cell: (86.49, 125.55, 102.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     P      54     15.00
     O    2004      8.00
     N    1833      7.00
     C    6240      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.15
  Conformation dependent library (CDL) restraints added in 301.5 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 6 sheets defined
      76.9% alpha, 4.2% beta
      21 base pairs and 36 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'B' and resid 4 through 13
      removed outlier: 4.442A  pdb=" N   LEU B  10 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   GLY B  11 " --> pdb=" O   LEU B   8 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS B  13 " --> pdb=" O   LEU B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 45
    Processing helix  chain 'B' and resid 51 through 67
      removed outlier: 4.518A  pdb=" N   GLY B  55 " --> pdb=" O   ASP B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 75
    Processing helix  chain 'B' and resid 76 through 86
    Processing helix  chain 'B' and resid 99 through 104
      removed outlier: 4.292A  pdb=" N   VAL B 103 " --> pdb=" O   ARG B  99 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE B 104 " --> pdb=" O   PHE B 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 99 through 104'
    Processing helix  chain 'B' and resid 110 through 118
    Processing helix  chain 'B' and resid 129 through 139
    Processing helix  chain 'B' and resid 148 through 165
    Processing helix  chain 'B' and resid 171 through 175
    Processing helix  chain 'B' and resid 176 through 190
    Processing helix  chain 'B' and resid 190 through 204
      removed outlier: 4.080A  pdb=" N   LYS B 194 " --> pdb=" O   SER B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 223
    Processing helix  chain 'B' and resid 227 through 237
    Processing helix  chain 'B' and resid 249 through 252
      removed outlier: 3.673A  pdb=" N   ARG B 252 " --> pdb=" O   PRO B 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 249 through 252'
    Processing helix  chain 'B' and resid 253 through 272
      removed outlier: 4.132A  pdb=" N   GLU B 259 " --> pdb=" O   LYS B 255 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ARG B 272 " --> pdb=" O   SER B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 278
      No H-bonds generated for 'chain 'B' and resid 276 through 278'
    Processing helix  chain 'B' and resid 279 through 284
    Processing helix  chain 'B' and resid 287 through 292
      removed outlier: 3.659A  pdb=" N   GLU B 292 " --> pdb=" O   ASN B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 311
    Processing helix  chain 'B' and resid 312 through 317
    Processing helix  chain 'B' and resid 323 through 350
      removed outlier: 3.782A  pdb=" N   ALA B 350 " --> pdb=" O   ILE B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 391
      removed outlier: 3.509A  pdb=" N   ARG B 356 " --> pdb=" O   ASP B 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4 through 13
      removed outlier: 4.442A  pdb=" N   LEU A  10 " --> pdb=" O   LEU A   7 " (cutoff:3.500A)
      removed outlier: 5.539A  pdb=" N   GLY A  11 " --> pdb=" O   LEU A   8 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS A  13 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 45
    Processing helix  chain 'A' and resid 51 through 67
      removed outlier: 4.519A  pdb=" N   GLY A  55 " --> pdb=" O   ASP A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 75
    Processing helix  chain 'A' and resid 76 through 86
    Processing helix  chain 'A' and resid 99 through 104
      removed outlier: 4.292A  pdb=" N   VAL A 103 " --> pdb=" O   ARG A  99 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE A 104 " --> pdb=" O   PHE A 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 99 through 104'
    Processing helix  chain 'A' and resid 110 through 118
    Processing helix  chain 'A' and resid 129 through 139
    Processing helix  chain 'A' and resid 148 through 165
    Processing helix  chain 'A' and resid 171 through 175
    Processing helix  chain 'A' and resid 176 through 190
    Processing helix  chain 'A' and resid 190 through 204
      removed outlier: 4.080A  pdb=" N   LYS A 194 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 223
    Processing helix  chain 'A' and resid 227 through 237
    Processing helix  chain 'A' and resid 249 through 252
      removed outlier: 3.673A  pdb=" N   ARG A 252 " --> pdb=" O   PRO A 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 249 through 252'
    Processing helix  chain 'A' and resid 253 through 272
      removed outlier: 4.132A  pdb=" N   GLU A 259 " --> pdb=" O   LYS A 255 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ARG A 272 " --> pdb=" O   SER A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 278
      No H-bonds generated for 'chain 'A' and resid 276 through 278'
    Processing helix  chain 'A' and resid 279 through 284
    Processing helix  chain 'A' and resid 287 through 292
      removed outlier: 3.659A  pdb=" N   GLU A 292 " --> pdb=" O   ASN A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 311
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 323 through 350
      removed outlier: 3.782A  pdb=" N   ALA A 350 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 391
      removed outlier: 3.509A  pdb=" N   ARG A 356 " --> pdb=" O   ASP A 352 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 13
      removed outlier: 4.441A  pdb=" N   LEU C  10 " --> pdb=" O   LEU C   7 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   GLY C  11 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   LYS C  13 " --> pdb=" O   LEU C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 31 through 45
    Processing helix  chain 'C' and resid 51 through 67
      removed outlier: 4.518A  pdb=" N   GLY C  55 " --> pdb=" O   ASP C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 75
    Processing helix  chain 'C' and resid 76 through 86
    Processing helix  chain 'C' and resid 99 through 104
      removed outlier: 4.292A  pdb=" N   VAL C 103 " --> pdb=" O   ARG C  99 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE C 104 " --> pdb=" O   PHE C 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 99 through 104'
    Processing helix  chain 'C' and resid 110 through 118
    Processing helix  chain 'C' and resid 129 through 139
    Processing helix  chain 'C' and resid 148 through 165
    Processing helix  chain 'C' and resid 171 through 175
    Processing helix  chain 'C' and resid 176 through 190
    Processing helix  chain 'C' and resid 190 through 204
      removed outlier: 4.081A  pdb=" N   LYS C 194 " --> pdb=" O   SER C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 223
    Processing helix  chain 'C' and resid 227 through 237
    Processing helix  chain 'C' and resid 249 through 252
      removed outlier: 3.673A  pdb=" N   ARG C 252 " --> pdb=" O   PRO C 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 249 through 252'
    Processing helix  chain 'C' and resid 253 through 272
      removed outlier: 4.131A  pdb=" N   GLU C 259 " --> pdb=" O   LYS C 255 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ARG C 272 " --> pdb=" O   SER C 268 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 276 through 278
      No H-bonds generated for 'chain 'C' and resid 276 through 278'
    Processing helix  chain 'C' and resid 279 through 284
    Processing helix  chain 'C' and resid 287 through 292
      removed outlier: 3.659A  pdb=" N   GLU C 292 " --> pdb=" O   ASN C 289 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 296 through 311
    Processing helix  chain 'C' and resid 312 through 317
    Processing helix  chain 'C' and resid 323 through 350
      removed outlier: 3.783A  pdb=" N   ALA C 350 " --> pdb=" O   ILE C 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 352 through 391
      removed outlier: 3.509A  pdb=" N   ARG C 356 " --> pdb=" O   ASP C 352 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 22 through 27
    Processing sheet with id=AA2, first strand: chain 'B' and resid 238 through 241
    Processing sheet with id=AA3, first strand: chain 'A' and resid 22 through 27
    Processing sheet with id=AA4, first strand: chain 'A' and resid 238 through 241
    Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 27
    Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 241

    609 hydrogen bonds defined for protein.
    1719 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      42 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      21 basepair parallelities
      36 stacking parallelities
  Total time for adding SS restraints: 1.31

  Time building geometry restraints manager: 1.35 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:             11.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     10.130
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
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= 0.154
  Angle     :  0.612   7.587  14404  Z= 0.332
  Chirality :  0.038   0.140   1722
  Planarity :  0.005   0.049   1632
  Dihedral  : 15.199  87.158   4059
  Min Nonbonded Distance : 0.014

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

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

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.15 (10450)
  covalent geometry    : angle       0.61221 /  0.33 (14404)
  hydrogen bonds       : bond        0.17407 / 11.29 (  651)
  hydrogen bonds       : angle       5.99784 /  4.27 ( 1719)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 382
  time to evaluate  : 0.259 
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: 0.9228 (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: 0.1028
  time to fit residues: 51.5568
Evaluate side-chains
  318 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 318
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  64 HIS
** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 GLN
** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  18 HIS
A  64 HIS
** A 158 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
C 380 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.158532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.135362 restraints weight = 20231.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 3.76
r_work: 0.3658 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3655
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3655 r_free = 0.3655    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3637 r_free = 0.3637    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (14 function evaluations)
r_final: 0.3637
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.5945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.037   1.154  10450  Z= 2.465
  Angle     :  4.421  82.252  14404  Z= 2.332
  Chirality :  0.388   5.329   1722
  Planarity :  0.014   0.137   1632
  Dihedral  : 23.660 139.020   1932
  Min Nonbonded Distance : 1.177

Molprobity Statistics.
  All-atom Clashscore : 51.57
  Ramachandran Plot:
    Outliers :  0.53 %
    Allowed  :  3.64 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.31 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.84 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.25), residues: 1125
  helix:  1.32 (0.19), residues: 696
  sheet: -1.69 (0.88), residues: 30
  loop : -0.96 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.029   0.002   ARG C 281 
 TYR   0.038   0.002   TYR A 211 
 PHE   0.019   0.002   PHE C 195 
 TRP   0.006   0.001   TRP A 174 
 HIS   0.030   0.002   HIS C 293 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.03737 /  2.46 (10450)
  covalent geometry    : angle       4.42069 /  2.33 (14404)
  hydrogen bonds       : bond        0.63289 / 39.31 (  651)
  hydrogen bonds       : angle       5.81814 /  4.14 ( 1719)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  362 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 334
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.6736 (m-80) cc_final: 0.6357 (m-80)
REVERT: B   80 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8074 (mtmm)
REVERT: B   81 TYR cc_start: 0.8532 (t80) cc_final: 0.8271 (t80)
REVERT: B  180 MET cc_start: 0.8807 (mpp) cc_final: 0.8449 (mpp)
REVERT: B  198 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.8989 (mp)
REVERT: B  212 ASP cc_start: 0.8985 (m-30) cc_final: 0.8657 (m-30)
REVERT: B  322 GLN cc_start: 0.9213 (pm20) cc_final: 0.8952 (pm20)
REVERT: B  325 GLN cc_start: 0.8642 (mp10) cc_final: 0.8399 (mp10)
REVERT: B  340 ARG cc_start: 0.8467 (tpt90) cc_final: 0.8122 (mmm160)
REVERT: B  345 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8325 (mm-30)
REVERT: B  380 GLN cc_start: 0.9031 (tp40) cc_final: 0.8782 (tp40)
REVERT: A   47 ILE cc_start: 0.9229 (mm) cc_final: 0.8901 (mp)
REVERT: A   71 ASP cc_start: 0.8533 (t0) cc_final: 0.8311 (t0)
REVERT: A  198 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.8952 (mp)
REVERT: A  212 ASP cc_start: 0.8872 (m-30) cc_final: 0.8575 (m-30)
REVERT: A  323 TYR cc_start: 0.8991 (m-80) cc_final: 0.8740 (m-80)
REVERT: A  342 GLU cc_start: 0.8300 (pp20) cc_final: 0.7950 (pp20)
REVERT: A  345 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8306 (mm-30)
REVERT: A  380 GLN cc_start: 0.9145 (tp-100) cc_final: 0.8860 (tp40)
REVERT: A  383 GLU cc_start: 0.8642 (tm-30) cc_final: 0.8089 (tm-30)
REVERT: C   32 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8519 (tp-100)
REVERT: C   65 TYR cc_start: 0.6964 (m-10) cc_final: 0.6677 (m-80)
REVERT: C   80 LYS cc_start: 0.8498 (mtmm) cc_final: 0.8107 (mtmm)
REVERT: C  164 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7916 (tt0)
REVERT: C  180 MET cc_start: 0.8835 (mpp) cc_final: 0.8461 (mpp)
REVERT: C  198 ILE cc_start: 0.9380 (OUTLIER) cc_final: 0.9026 (mp)
REVERT: C  275 GLU cc_start: 0.8957 (mp0) cc_final: 0.8737 (mp0)
REVERT: C  325 GLN cc_start: 0.8839 (mp10) cc_final: 0.8605 (mp10)
REVERT: C  345 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8385 (mm-30)
REVERT: C  356 ARG cc_start: 0.7752 (mmt-90) cc_final: 0.7301 (mmt-90)
REVERT: C  357 LYS cc_start: 0.9061 (mtmm) cc_final: 0.8838 (mtmm)
  outliers start: 28
  outliers final: 10
  residues processed: 353
  average time/residue: 0.1000
  time to fit residues: 46.6612
Evaluate side-chains
  336 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 323
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  197 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  232 THR
Chi-restraints excluded: chain C residue  317 VAL
Chi-restraints excluded: chain C residue  380 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 113 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   chunk 101 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 108 optimal weight:    2.9990
   chunk 39 optimal weight:   20.0000
   chunk 21 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.9786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 310 HIS
C  21 ASN
C  37 ASN
C  64 HIS
** C 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 324 GLN
C 380 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.162027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.137813 restraints weight = 19849.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 3.84
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3893
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3893 r_free = 0.3893    target_work(ls_wunit_k1) = 0.146         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       22 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3890 r_free = 0.3890    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 8 (13 function evaluations)
r_final: 0.3890
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.7579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.020   0.393  10450  Z= 1.274
  Angle     :  3.103  68.419  14404  Z= 1.649
  Chirality :  0.326   4.885   1722
  Planarity :  0.012   0.220   1632
  Dihedral  : 21.456 172.309   1932
  Min Nonbonded Distance : 1.551

Molprobity Statistics.
  All-atom Clashscore : 56.22
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.27 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 17.53 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.25), residues: 1125
  helix:  0.91 (0.19), residues: 726
  sheet: -1.84 (0.89), residues: 30
  loop : -1.41 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.002   ARG C 281 
 TYR   0.046   0.003   TYR A 211 
 PHE   0.017   0.002   PHE C 195 
 TRP   0.006   0.001   TRP B 174 
 HIS   0.019   0.002   HIS C 162 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01982 /  1.27 (10450)
  covalent geometry    : angle       3.10302 /  1.65 (14404)
  hydrogen bonds       : bond        0.69613 / 45.75 (  651)
  hydrogen bonds       : angle       5.56368 /  4.00 ( 1719)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  425 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 368
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.6516 (m-80) cc_final: 0.6211 (m-80)
REVERT: B   88 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8088 (mm-30)
REVERT: B  133 PHE cc_start: 0.8590 (t80) cc_final: 0.8385 (t80)
REVERT: B  180 MET cc_start: 0.8661 (mpp) cc_final: 0.8415 (mpp)
REVERT: B  198 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9076 (mp)
REVERT: B  212 ASP cc_start: 0.8572 (m-30) cc_final: 0.8179 (m-30)
REVERT: B  252 ARG cc_start: 0.8068 (mmt90) cc_final: 0.7816 (mmt90)
REVERT: B  288 ILE cc_start: 0.8823 (tp) cc_final: 0.8450 (tp)
REVERT: B  319 VAL cc_start: 0.2650 (OUTLIER) cc_final: 0.2430 (t)
REVERT: B  345 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8257 (mm-30)
REVERT: B  356 ARG cc_start: 0.7684 (mmt-90) cc_final: 0.7394 (mmt-90)
REVERT: B  380 GLN cc_start: 0.8820 (tp40) cc_final: 0.8528 (tp40)
REVERT: B  383 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8123 (tm-30)
REVERT: A   65 TYR cc_start: 0.5627 (m-80) cc_final: 0.5344 (m-80)
REVERT: A   80 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8029 (mtmm)
REVERT: A   84 ASP cc_start: 0.8041 (m-30) cc_final: 0.7754 (m-30)
REVERT: A  173 HIS cc_start: 0.7705 (t70) cc_final: 0.7492 (t70)
REVERT: A  198 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9064 (mp)
REVERT: A  252 ARG cc_start: 0.8265 (mmt90) cc_final: 0.8045 (mmt90)
REVERT: A  308 THR cc_start: 0.8354 (m) cc_final: 0.8020 (m)
REVERT: A  323 TYR cc_start: 0.8908 (m-80) cc_final: 0.8570 (m-80)
REVERT: A  342 GLU cc_start: 0.8240 (pp20) cc_final: 0.7777 (pp20)
REVERT: A  345 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8231 (mm-30)
REVERT: A  356 ARG cc_start: 0.7594 (mmt-90) cc_final: 0.7180 (mmt-90)
REVERT: A  383 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7969 (tm-30)
REVERT: C   32 GLN cc_start: 0.8783 (tp-100) cc_final: 0.8530 (tp-100)
REVERT: C  149 ARG cc_start: 0.7936 (mmm160) cc_final: 0.7584 (mmm160)
REVERT: C  180 MET cc_start: 0.8624 (mpp) cc_final: 0.8370 (mpp)
REVERT: C  198 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9102 (mp)
REVERT: C  252 ARG cc_start: 0.8226 (mmt90) cc_final: 0.7909 (mmt90)
REVERT: C  275 GLU cc_start: 0.8473 (mp0) cc_final: 0.8259 (mp0)
REVERT: C  288 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8361 (tp)
REVERT: C  325 GLN cc_start: 0.8724 (mp10) cc_final: 0.8462 (mp10)
REVERT: C  343 HIS cc_start: 0.8252 (t-90) cc_final: 0.7913 (t-90)
REVERT: C  345 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8262 (mm-30)
REVERT: C  352 ASP cc_start: 0.8448 (p0) cc_final: 0.7993 (p0)
REVERT: C  354 GLU cc_start: 0.9011 (tp30) cc_final: 0.8570 (tp30)
REVERT: C  356 ARG cc_start: 0.7540 (mmt-90) cc_final: 0.6669 (mpt180)
REVERT: C  357 LYS cc_start: 0.8989 (mtmm) cc_final: 0.8416 (mttp)
REVERT: C  380 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8603 (tp-100)
  outliers start: 57
  outliers final: 21
  residues processed: 400
  average time/residue: 0.0954
  time to fit residues: 51.2939
Evaluate side-chains
  359 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 332
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
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  144 LEU
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  317 VAL
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain A residue   31 HIS
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  288 ILE
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  313 THR
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 31 optimal weight:    7.9990
   chunk 53 optimal weight:    0.7980
   chunk 101 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 110 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    1.0584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 GLN
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  37 ASN
C  64 HIS
C  74 ASN
** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.167046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.142417 restraints weight = 19386.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3925 rms_B_bonded: 3.76
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3928
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3928 r_free = 0.3928    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3925 r_free = 0.3925    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (27 function evaluations)
r_final: 0.3925
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.8545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.257  10450  Z= 0.808
  Angle     :  2.398  46.190  14404  Z= 1.266
  Chirality :  0.277   4.773   1722
  Planarity :  0.009   0.074   1632
  Dihedral  : 21.357 179.740   1932
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 59.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 19.78 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.45 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.25), residues: 1125
  helix:  0.79 (0.19), residues: 720
  sheet: -2.14 (0.86), residues: 30
  loop : -1.49 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.034   0.002   ARG C 188 
 TYR   0.045   0.004   TYR C  65 
 PHE   0.039   0.002   PHE C 184 
 TRP   0.005   0.001   TRP A 174 
 HIS   0.019   0.001   HIS B 162 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01304 /  0.81 (10450)
  covalent geometry    : angle       2.39761 /  1.27 (14404)
  hydrogen bonds       : bond        0.59370 / 38.16 (  651)
  hydrogen bonds       : angle       5.38889 /  3.85 ( 1719)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  418 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 369
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   80 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8244 (mtmm)
REVERT: B   88 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7808 (mm-30)
REVERT: B  133 PHE cc_start: 0.8497 (t80) cc_final: 0.8206 (t80)
REVERT: B  158 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7472 (mm110)
REVERT: B  180 MET cc_start: 0.8718 (mpp) cc_final: 0.8408 (mpp)
REVERT: B  194 LYS cc_start: 0.8907 (mttm) cc_final: 0.8335 (mttm)
REVERT: B  198 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9063 (mp)
REVERT: B  252 ARG cc_start: 0.8071 (mmt90) cc_final: 0.7735 (mmt90)
REVERT: B  259 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8140 (mm-30)
REVERT: B  308 THR cc_start: 0.7944 (m) cc_final: 0.7557 (m)
REVERT: B  324 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8423 (mm-40)
REVERT: B  327 ARG cc_start: 0.8001 (ttp-110) cc_final: 0.7624 (ttp-110)
REVERT: B  336 LYS cc_start: 0.9186 (mptt) cc_final: 0.8950 (mmtp)
REVERT: B  345 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8220 (mm-30)
REVERT: B  356 ARG cc_start: 0.7615 (mmt-90) cc_final: 0.7357 (mmt-90)
REVERT: B  380 GLN cc_start: 0.8855 (tp-100) cc_final: 0.8529 (tp40)
REVERT: B  383 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8191 (tm-30)
REVERT: B  384 LYS cc_start: 0.9266 (mttm) cc_final: 0.8780 (mttt)
REVERT: A   64 HIS cc_start: 0.8756 (t-90) cc_final: 0.8549 (t70)
REVERT: A   80 LYS cc_start: 0.8451 (mtmm) cc_final: 0.7987 (mtmm)
REVERT: A   84 ASP cc_start: 0.7958 (m-30) cc_final: 0.7686 (m-30)
REVERT: A  163 GLN cc_start: 0.8349 (pt0) cc_final: 0.8105 (pp30)
REVERT: A  198 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9105 (mp)
REVERT: A  228 LEU cc_start: 0.6730 (tp) cc_final: 0.6522 (tp)
REVERT: A  252 ARG cc_start: 0.8312 (mmt90) cc_final: 0.8081 (mmt90)
REVERT: A  308 THR cc_start: 0.8073 (m) cc_final: 0.7449 (m)
REVERT: A  324 GLN cc_start: 0.8592 (mm-40) cc_final: 0.7990 (mm-40)
REVERT: A  345 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8244 (mm-30)
REVERT: A  356 ARG cc_start: 0.7585 (mmt-90) cc_final: 0.7195 (mmt-90)
REVERT: A  368 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8589 (tm-30)
REVERT: A  383 GLU cc_start: 0.8416 (tm-30) cc_final: 0.7998 (tm-30)
REVERT: C   32 GLN cc_start: 0.8803 (tp-100) cc_final: 0.8568 (tp-100)
REVERT: C   61 CYS cc_start: 0.8357 (t) cc_final: 0.8085 (t)
REVERT: C   64 HIS cc_start: 0.8853 (t-90) cc_final: 0.8622 (t-90)
REVERT: C   65 TYR cc_start: 0.6219 (m-80) cc_final: 0.5897 (m-80)
REVERT: C   80 LYS cc_start: 0.8507 (mtmm) cc_final: 0.8260 (mtmm)
REVERT: C  153 GLU cc_start: 0.8259 (mm-30) cc_final: 0.8009 (mm-30)
REVERT: C  198 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9131 (mp)
REVERT: C  252 ARG cc_start: 0.8195 (mmt90) cc_final: 0.7899 (mmt90)
REVERT: C  255 LYS cc_start: 0.3400 (mmtt) cc_final: 0.2813 (mmtt)
REVERT: C  345 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8279 (mm-30)
REVERT: C  356 ARG cc_start: 0.7469 (mmt-90) cc_final: 0.6752 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8776 (mtmm) cc_final: 0.8289 (mtmm)
REVERT: C  360 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8071 (mt-10)
REVERT: C  383 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8172 (tm-30)
  outliers start: 49
  outliers final: 23
  residues processed: 389
  average time/residue: 0.1062
  time to fit residues: 54.5677
Evaluate side-chains
  360 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 332
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
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  130 ILE
Chi-restraints excluded: chain B residue  158 GLN
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  324 GLN
Chi-restraints excluded: chain B residue  388 LEU
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  198 ILE
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  313 THR
Chi-restraints excluded: chain C residue  314 LEU
Chi-restraints excluded: chain C residue  319 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 57 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 101 optimal weight:    0.8980
   chunk 40 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 103 optimal weight:    0.6980
   chunk 90 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  64 HIS
** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 217 ASN
A 284 ASN
A 318 ASN
A 380 GLN
C  37 ASN
** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.170212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.144366 restraints weight = 19280.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 3.91
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3949
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3949 r_free = 0.3949    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3951 r_free = 0.3951    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (16 function evaluations)
r_final: 0.3951
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.9174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.190  10450  Z= 0.650
  Angle     :  2.048  44.153  14404  Z= 1.097
  Chirality :  0.242   4.633   1722
  Planarity :  0.007   0.075   1632
  Dihedral  : 21.524 179.026   1932
  Min Nonbonded Distance : 1.676

Molprobity Statistics.
  All-atom Clashscore : 50.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 21.20 %
    Favored  : 73.29 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.25), residues: 1125
  helix:  0.51 (0.18), residues: 738
  sheet: -1.13 (0.62), residues: 78
  loop : -1.35 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.027   0.001   ARG C 327 
 TYR   0.046   0.003   TYR B  65 
 PHE   0.069   0.002   PHE C 184 
 TRP   0.006   0.001   TRP A 174 
 HIS   0.011   0.001   HIS C 162 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01055 /  0.65 (10450)
  covalent geometry    : angle       2.04830 /  1.10 (14404)
  hydrogen bonds       : bond        0.55662 / 35.76 (  651)
  hydrogen bonds       : angle       5.22027 /  3.74 ( 1719)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  411 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 357
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   65 TYR cc_start: 0.6218 (m-80) cc_final: 0.5727 (m-80)
REVERT: B  133 PHE cc_start: 0.8437 (t80) cc_final: 0.8152 (t80)
REVERT: B  188 ARG cc_start: 0.8653 (tpt170) cc_final: 0.8139 (ttt90)
REVERT: B  194 LYS cc_start: 0.8929 (mttm) cc_final: 0.8364 (mttm)
REVERT: B  198 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9065 (mp)
REVERT: B  252 ARG cc_start: 0.8097 (mmt90) cc_final: 0.7684 (mmt90)
REVERT: B  259 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7783 (mm-30)
REVERT: B  308 THR cc_start: 0.7964 (m) cc_final: 0.7430 (m)
REVERT: B  319 VAL cc_start: 0.3241 (OUTLIER) cc_final: 0.2505 (t)
REVERT: B  332 ASP cc_start: 0.8872 (m-30) cc_final: 0.8614 (m-30)
REVERT: B  336 LYS cc_start: 0.9196 (mptt) cc_final: 0.8976 (mmtp)
REVERT: B  345 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8428 (mm-30)
REVERT: B  356 ARG cc_start: 0.7637 (mmt-90) cc_final: 0.7217 (mmt-90)
REVERT: B  380 GLN cc_start: 0.8841 (tp-100) cc_final: 0.8547 (tp40)
REVERT: B  383 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8173 (tm-30)
REVERT: A    2 MET cc_start: 0.8376 (ppp) cc_final: 0.8050 (ppp)
REVERT: A   44 ASN cc_start: 0.9164 (p0) cc_final: 0.8779 (p0)
REVERT: A   80 LYS cc_start: 0.8443 (mtmm) cc_final: 0.7930 (mtmm)
REVERT: A   84 ASP cc_start: 0.7932 (m-30) cc_final: 0.7639 (m-30)
REVERT: A  157 ARG cc_start: 0.8466 (ttm170) cc_final: 0.8066 (ttm170)
REVERT: A  163 GLN cc_start: 0.8393 (pt0) cc_final: 0.8095 (pp30)
REVERT: A  198 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9119 (mp)
REVERT: A  231 LYS cc_start: 0.9023 (ptmt) cc_final: 0.8745 (ptpt)
REVERT: A  252 ARG cc_start: 0.8323 (mmt90) cc_final: 0.8014 (mmt90)
REVERT: A  259 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8182 (mm-30)
REVERT: A  308 THR cc_start: 0.8076 (m) cc_final: 0.7428 (m)
REVERT: A  345 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8291 (mm-30)
REVERT: A  354 GLU cc_start: 0.8682 (tp30) cc_final: 0.8221 (pt0)
REVERT: A  356 ARG cc_start: 0.7587 (mmt-90) cc_final: 0.7155 (mmt-90)
REVERT: A  365 GLN cc_start: 0.8999 (tp40) cc_final: 0.8694 (tp40)
REVERT: A  368 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8508 (tm-30)
REVERT: A  383 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8214 (tm-30)
REVERT: C   64 HIS cc_start: 0.8657 (t-90) cc_final: 0.8426 (t-90)
REVERT: C   65 TYR cc_start: 0.6366 (m-80) cc_final: 0.6098 (m-80)
REVERT: C   80 LYS cc_start: 0.8487 (mtmm) cc_final: 0.8093 (mtmm)
REVERT: C  153 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7979 (mm-30)
REVERT: C  198 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9115 (mp)
REVERT: C  252 ARG cc_start: 0.8312 (mmt90) cc_final: 0.7937 (mmt90)
REVERT: C  255 LYS cc_start: 0.3265 (mmtt) cc_final: 0.2384 (mmtt)
REVERT: C  257 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8752 (mmmm)
REVERT: C  345 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8321 (mm-30)
REVERT: C  354 GLU cc_start: 0.8927 (tp30) cc_final: 0.8028 (tp30)
REVERT: C  356 ARG cc_start: 0.7523 (mmt-90) cc_final: 0.6830 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8808 (mtmm) cc_final: 0.8330 (mtmm)
REVERT: C  380 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8586 (tp-100)
REVERT: C  382 ARG cc_start: 0.8742 (mmp80) cc_final: 0.8508 (mmp80)
  outliers start: 54
  outliers final: 28
  residues processed: 386
  average time/residue: 0.1048
  time to fit residues: 53.8185
Evaluate side-chains
  371 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 339
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
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  158 GLN
Chi-restraints excluded: chain B residue  161 VAL
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  232 THR
Chi-restraints excluded: chain B residue  247 LEU
Chi-restraints excluded: chain B residue  300 SER
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain A residue   48 ASP
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  227 LEU
Chi-restraints excluded: chain A residue  284 ASN
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  381 LYS
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  319 VAL
Chi-restraints excluded: chain C residue  374 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 115 optimal weight:    9.9990
   chunk 19 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 380 GLN
A  32 GLN
** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.171688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.145677 restraints weight = 19395.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3966 rms_B_bonded: 4.00
r_work (final): 0.3966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3966
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3966 r_free = 0.3966    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3967 r_free = 0.3967    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (13 function evaluations)
r_final: 0.3967
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.9694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.177  10450  Z= 0.584
  Angle     :  1.834  36.382  14404  Z= 0.997
  Chirality :  0.220   4.605   1722
  Planarity :  0.007   0.099   1632
  Dihedral  : 21.342 178.013   1932
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 50.18
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  4.80 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 23.85 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.25), residues: 1125
  helix:  0.52 (0.19), residues: 726
  sheet: -2.48 (0.86), residues: 30
  loop : -1.43 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 382 
 TYR   0.033   0.003   TYR A  65 
 PHE   0.049   0.003   PHE C 184 
 TRP   0.007   0.001   TRP A 174 
 HIS   0.015   0.001   HIS A 293 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00959 /  0.58 (10450)
  covalent geometry    : angle       1.83447 /  1.00 (14404)
  hydrogen bonds       : bond        0.51638 / 33.41 (  651)
  hydrogen bonds       : angle       5.20454 /  3.71 ( 1719)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  388 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 348
  time to evaluate  : 0.206 
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   80 LYS cc_start: 0.8477 (mtmm) cc_final: 0.8115 (mtmm)
REVERT: B  133 PHE cc_start: 0.8524 (t80) cc_final: 0.8261 (t80)
REVERT: B  188 ARG cc_start: 0.8586 (tpt170) cc_final: 0.8256 (ttt90)
REVERT: B  194 LYS cc_start: 0.8974 (mttm) cc_final: 0.8604 (mttm)
REVERT: B  198 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9082 (mp)
REVERT: B  308 THR cc_start: 0.7925 (m) cc_final: 0.7384 (m)
REVERT: B  327 ARG cc_start: 0.7821 (ttp-110) cc_final: 0.7610 (ttp-110)
REVERT: B  345 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8385 (mm-30)
REVERT: B  356 ARG cc_start: 0.7638 (mmt-90) cc_final: 0.7157 (mmt-90)
REVERT: B  357 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8443 (mtmm)
REVERT: B  365 GLN cc_start: 0.8864 (tp40) cc_final: 0.8467 (tp-100)
REVERT: B  380 GLN cc_start: 0.8908 (tp40) cc_final: 0.8647 (tp40)
REVERT: B  383 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8159 (tm-30)
REVERT: A    3 ASP cc_start: 0.9098 (t0) cc_final: 0.8779 (t0)
REVERT: A   44 ASN cc_start: 0.9178 (p0) cc_final: 0.8807 (p0)
REVERT: A   80 LYS cc_start: 0.8420 (mtmm) cc_final: 0.7940 (mtmm)
REVERT: A   81 TYR cc_start: 0.8529 (t80) cc_final: 0.8282 (t80)
REVERT: A   84 ASP cc_start: 0.7954 (m-30) cc_final: 0.7655 (m-30)
REVERT: A  163 GLN cc_start: 0.8416 (pt0) cc_final: 0.8104 (pp30)
REVERT: A  198 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9097 (mp)
REVERT: A  231 LYS cc_start: 0.8989 (ptmt) cc_final: 0.8726 (ptpt)
REVERT: A  252 ARG cc_start: 0.8280 (mmt90) cc_final: 0.7963 (mmt90)
REVERT: A  259 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7983 (mm-30)
REVERT: A  308 THR cc_start: 0.8009 (m) cc_final: 0.7509 (m)
REVERT: A  345 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8345 (mm-30)
REVERT: A  356 ARG cc_start: 0.7697 (mmt-90) cc_final: 0.7236 (mmt-90)
REVERT: A  365 GLN cc_start: 0.8991 (tp40) cc_final: 0.8739 (tp40)
REVERT: A  382 ARG cc_start: 0.8582 (mmp80) cc_final: 0.7912 (mmp-170)
REVERT: C    3 ASP cc_start: 0.8802 (t0) cc_final: 0.8549 (t0)
REVERT: C   32 GLN cc_start: 0.8734 (tp-100) cc_final: 0.8411 (tp-100)
REVERT: C   80 LYS cc_start: 0.8489 (mtmm) cc_final: 0.8080 (mtmm)
REVERT: C  194 LYS cc_start: 0.8696 (mttm) cc_final: 0.8269 (mttm)
REVERT: C  198 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9060 (mp)
REVERT: C  252 ARG cc_start: 0.8295 (mmt90) cc_final: 0.7869 (mmt90)
REVERT: C  255 LYS cc_start: 0.3268 (mmtt) cc_final: 0.2417 (mmtt)
REVERT: C  257 LYS cc_start: 0.9104 (mmmm) cc_final: 0.8733 (mmmm)
REVERT: C  345 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8309 (mm-30)
REVERT: C  354 GLU cc_start: 0.8941 (tp30) cc_final: 0.8093 (tp30)
REVERT: C  356 ARG cc_start: 0.7553 (mmt-90) cc_final: 0.6812 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8781 (mtmm) cc_final: 0.8330 (mtmm)
REVERT: C  380 GLN cc_start: 0.8792 (tp-100) cc_final: 0.8509 (tp-100)
REVERT: C  382 ARG cc_start: 0.8783 (mmp80) cc_final: 0.8503 (mmp80)
  outliers start: 40
  outliers final: 26
  residues processed: 364
  average time/residue: 0.0961
  time to fit residues: 46.5139
Evaluate side-chains
  357 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 328
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
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  139 LEU
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  314 LEU
Chi-restraints excluded: chain B residue  343 HIS
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  144 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  381 LYS
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  144 LEU
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  209 ASP
Chi-restraints excluded: chain C residue  319 VAL
Chi-restraints excluded: chain C residue  374 THR
Chi-restraints excluded: chain C residue  378 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 115 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 61 optimal weight:    0.7980
   chunk 114 optimal weight:    5.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 318 ASN
** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.174679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.148879 restraints weight = 19014.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 3.80
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4017 r_free = 0.4017    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4017 r_free = 0.4017    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 6 (19 function evaluations)
r_final: 0.4017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          1.0325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.164  10450  Z= 0.536
  Angle     :  1.778  47.156  14404  Z= 0.943
  Chirality :  0.213   4.879   1722
  Planarity :  0.007   0.106   1632
  Dihedral  : 21.356 178.622   1932
  Min Nonbonded Distance : 1.828

Molprobity Statistics.
  All-atom Clashscore : 47.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 25.28 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.25), residues: 1125
  helix:  0.35 (0.19), residues: 747
  sheet: -1.59 (0.59), residues: 72
  loop : -1.07 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 387 
 TYR   0.053   0.004   TYR B 296 
 PHE   0.044   0.003   PHE C 184 
 TRP   0.010   0.001   TRP A 174 
 HIS   0.016   0.001   HIS A 293 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00879 /  0.54 (10450)
  covalent geometry    : angle       1.77834 /  0.94 (14404)
  hydrogen bonds       : bond        0.47697 / 31.01 (  651)
  hydrogen bonds       : angle       5.26405 /  3.71 ( 1719)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 334
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  133 PHE cc_start: 0.8602 (t80) cc_final: 0.8369 (t80)
REVERT: B  173 HIS cc_start: 0.7719 (t-90) cc_final: 0.7464 (t-90)
REVERT: B  194 LYS cc_start: 0.8978 (mttm) cc_final: 0.8228 (mttm)
REVERT: B  252 ARG cc_start: 0.8149 (mmt90) cc_final: 0.7831 (mmt90)
REVERT: B  308 THR cc_start: 0.7808 (m) cc_final: 0.7321 (m)
REVERT: B  345 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8405 (mm-30)
REVERT: B  354 GLU cc_start: 0.8846 (tp30) cc_final: 0.8617 (tp30)
REVERT: B  356 ARG cc_start: 0.7692 (mmt-90) cc_final: 0.7225 (mmt-90)
REVERT: B  365 GLN cc_start: 0.8753 (tp40) cc_final: 0.8430 (tp-100)
REVERT: B  380 GLN cc_start: 0.8899 (tp40) cc_final: 0.8666 (tp40)
REVERT: B  383 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8120 (tm-30)
REVERT: A    2 MET cc_start: 0.8394 (ppp) cc_final: 0.8025 (ppp)
REVERT: A    3 ASP cc_start: 0.9007 (t0) cc_final: 0.8653 (t0)
REVERT: A   44 ASN cc_start: 0.9214 (p0) cc_final: 0.8851 (p0)
REVERT: A   80 LYS cc_start: 0.8427 (mtmm) cc_final: 0.7940 (mtmm)
REVERT: A   81 TYR cc_start: 0.8515 (t80) cc_final: 0.8303 (t80)
REVERT: A   84 ASP cc_start: 0.7960 (m-30) cc_final: 0.7677 (m-30)
REVERT: A  163 GLN cc_start: 0.8372 (pt0) cc_final: 0.7946 (pp30)
REVERT: A  198 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9088 (mp)
REVERT: A  308 THR cc_start: 0.7919 (m) cc_final: 0.7500 (m)
REVERT: A  345 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8267 (mm-30)
REVERT: A  354 GLU cc_start: 0.5523 (pt0) cc_final: 0.4533 (pt0)
REVERT: A  356 ARG cc_start: 0.7681 (mmt-90) cc_final: 0.7074 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8320 (pttp) cc_final: 0.7935 (mtmm)
REVERT: A  360 GLU cc_start: 0.8244 (mt-10) cc_final: 0.8035 (mt-10)
REVERT: A  365 GLN cc_start: 0.8942 (tp40) cc_final: 0.8684 (tp40)
REVERT: A  380 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.8474 (pp30)
REVERT: C   80 LYS cc_start: 0.8498 (mtmm) cc_final: 0.8104 (mtmm)
REVERT: C  180 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8356 (mpp)
REVERT: C  194 LYS cc_start: 0.8643 (mttm) cc_final: 0.8306 (mttm)
REVERT: C  198 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.9173 (mp)
REVERT: C  250 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8728 (tt)
REVERT: C  252 ARG cc_start: 0.8335 (mmt90) cc_final: 0.7997 (mmt90)
REVERT: C  255 LYS cc_start: 0.3141 (mmtt) cc_final: 0.2119 (mmtt)
REVERT: C  345 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8256 (mm-30)
REVERT: C  356 ARG cc_start: 0.7550 (mmt-90) cc_final: 0.6807 (mmt-90)
REVERT: C  357 LYS cc_start: 0.8791 (mtmm) cc_final: 0.8363 (mtmm)
  outliers start: 46
  outliers final: 27
  residues processed: 356
  average time/residue: 0.1068
  time to fit residues: 50.2193
Evaluate side-chains
  340 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 308
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
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   58 LEU
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  267 LEU
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain B residue  388 LEU
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  130 ILE
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  216 SER
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain A residue  380 GLN
Chi-restraints excluded: chain A residue  381 LYS
Chi-restraints excluded: chain C residue   30 ASN
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  180 MET
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  198 ILE
Chi-restraints excluded: chain C residue  209 ASP
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  319 VAL
Chi-restraints excluded: chain C residue  374 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 92 optimal weight:    7.9990
   chunk 41 optimal weight:    5.9990
   chunk 114 optimal weight:    6.9990
   chunk 90 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0670
   chunk 115 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 107 optimal weight:    0.5980
   chunk 86 optimal weight:    0.5980
   overall best weight:    0.8320

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  37 ASN
** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 284 ASN
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.176384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.150499 restraints weight = 19150.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.4038 rms_B_bonded: 3.84
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4039
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4039 r_free = 0.4039    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4039 r_free = 0.4039    target_work(ls_wunit_k1) = 0.150         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (12 function evaluations)
r_final: 0.4039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          1.0784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.158  10450  Z= 0.499
  Angle     :  1.717  51.214  14404  Z= 0.910
  Chirality :  0.210   4.812   1722
  Planarity :  0.008   0.091   1632
  Dihedral  : 21.424 178.377   1932
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 46.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 26.71 %
    Favored  : 69.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.25), residues: 1125
  helix:  0.35 (0.19), residues: 747
  sheet: -1.71 (0.56), residues: 72
  loop : -0.95 (0.39), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG A 281 
 TYR   0.027   0.003   TYR B  65 
 PHE   0.058   0.003   PHE C 184 
 TRP   0.005   0.001   TRP A 174 
 HIS   0.014   0.001   HIS A 293 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00853 /  0.50 (10450)
  covalent geometry    : angle       1.71702 /  0.91 (14404)
  hydrogen bonds       : bond        0.44709 / 29.09 (  651)
  hydrogen bonds       : angle       5.30631 /  3.79 ( 1719)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  374 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 337
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   80 LYS cc_start: 0.8538 (mtmm) cc_final: 0.8148 (mtmm)
REVERT: B  133 PHE cc_start: 0.8706 (t80) cc_final: 0.8477 (t80)
REVERT: B  173 HIS cc_start: 0.7707 (t-90) cc_final: 0.7455 (t-90)
REVERT: B  252 ARG cc_start: 0.8152 (mmt90) cc_final: 0.7711 (mmt90)
REVERT: B  345 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8459 (mm-30)
REVERT: B  355 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8138 (pm20)
REVERT: B  356 ARG cc_start: 0.7617 (mmt-90) cc_final: 0.7254 (mmt-90)
REVERT: B  365 GLN cc_start: 0.8807 (tp40) cc_final: 0.8591 (tp40)
REVERT: B  382 ARG cc_start: 0.8585 (mmp80) cc_final: 0.8336 (mmp-170)
REVERT: B  383 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8102 (tm-30)
REVERT: A    3 ASP cc_start: 0.9050 (t0) cc_final: 0.8743 (t0)
REVERT: A   65 TYR cc_start: 0.5732 (m-80) cc_final: 0.5426 (m-80)
REVERT: A   80 LYS cc_start: 0.8413 (mtmm) cc_final: 0.7932 (mtmm)
REVERT: A   81 TYR cc_start: 0.8499 (t80) cc_final: 0.8276 (t80)
REVERT: A   84 ASP cc_start: 0.8023 (m-30) cc_final: 0.7731 (m-30)
REVERT: A  163 GLN cc_start: 0.8399 (pt0) cc_final: 0.8000 (pp30)
REVERT: A  198 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9071 (mp)
REVERT: A  252 ARG cc_start: 0.8400 (mmm-85) cc_final: 0.7983 (mmt90)
REVERT: A  259 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8076 (mm-30)
REVERT: A  345 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8284 (mm-30)
REVERT: A  356 ARG cc_start: 0.7719 (mmt-90) cc_final: 0.7044 (mmt-90)
REVERT: C   80 LYS cc_start: 0.8490 (mtmm) cc_final: 0.8090 (mtmm)
REVERT: C  180 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8425 (mpp)
REVERT: C  194 LYS cc_start: 0.8699 (mttm) cc_final: 0.8230 (mttm)
REVERT: C  250 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8760 (tt)
REVERT: C  255 LYS cc_start: 0.3073 (mmtt) cc_final: 0.2212 (mmtt)
REVERT: C  345 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8244 (mm-30)
REVERT: C  357 LYS cc_start: 0.8718 (mtmm) cc_final: 0.8294 (mtmm)
  outliers start: 37
  outliers final: 26
  residues processed: 349
  average time/residue: 0.1039
  time to fit residues: 48.2811
Evaluate side-chains
  344 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 314
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   24 VAL
Chi-restraints excluded: chain B residue   30 ASN
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  355 GLU
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  141 LEU
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  216 SER
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  283 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  161 VAL
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain C residue  180 MET
Chi-restraints excluded: chain C residue  186 ILE
Chi-restraints excluded: chain C residue  197 LEU
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  319 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 71 optimal weight:    0.0870
   chunk 6 optimal weight:    0.9980
   chunk 87 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    0.7160

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  18 HIS
B 298 GLN
B 371 HIS
A 200 GLN
A 284 ASN
** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.178346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.152012 restraints weight = 19176.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 3.89
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4063
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4063 r_free = 0.4063    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4061 r_free = 0.4061    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.4061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          1.1169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.148  10450  Z= 0.476
  Angle     :  1.672  51.169  14404  Z= 0.882
  Chirality :  0.211   4.742   1722
  Planarity :  0.008   0.183   1632
  Dihedral  : 21.491 173.719   1932
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 44.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.33 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 27.73 %
    Favored  : 69.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.25), residues: 1125
  helix:  0.25 (0.19), residues: 747
  sheet: -2.71 (0.77), residues: 30
  loop : -0.92 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 188 
 TYR   0.032   0.003   TYR A 211 
 PHE   0.036   0.003   PHE A 184 
 TRP   0.007   0.001   TRP C 174 
 HIS   0.013   0.001   HIS A 293 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00822 /  0.48 (10450)
  covalent geometry    : angle       1.67228 /  0.88 (14404)
  hydrogen bonds       : bond        0.42888 / 27.95 (  651)
  hydrogen bonds       : angle       5.34503 /  3.81 ( 1719)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  357 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 325
  time to evaluate  : 0.266 
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   88 GLU cc_start: 0.8148 (tp30) cc_final: 0.7948 (tp30)
REVERT: B  173 HIS cc_start: 0.7749 (t-90) cc_final: 0.7484 (t-90)
REVERT: B  252 ARG cc_start: 0.8037 (mmt90) cc_final: 0.7755 (mmt90)
REVERT: B  345 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8444 (mm-30)
REVERT: B  356 ARG cc_start: 0.7638 (mmt-90) cc_final: 0.7055 (mmt-90)
REVERT: B  365 GLN cc_start: 0.8763 (tp40) cc_final: 0.8546 (tp40)
REVERT: B  383 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8140 (tm-30)
REVERT: A    3 ASP cc_start: 0.8981 (t0) cc_final: 0.8665 (t0)
REVERT: A   44 ASN cc_start: 0.9214 (p0) cc_final: 0.8851 (p0)
REVERT: A   47 ILE cc_start: 0.9125 (mm) cc_final: 0.8856 (mp)
REVERT: A   65 TYR cc_start: 0.5761 (m-80) cc_final: 0.5217 (m-80)
REVERT: A   80 LYS cc_start: 0.8394 (mtmm) cc_final: 0.7923 (mtmm)
REVERT: A   81 TYR cc_start: 0.8344 (t80) cc_final: 0.8131 (t80)
REVERT: A   84 ASP cc_start: 0.7958 (m-30) cc_final: 0.7670 (m-30)
REVERT: A  163 GLN cc_start: 0.8395 (pt0) cc_final: 0.8017 (pp30)
REVERT: A  181 LYS cc_start: 0.8503 (tptt) cc_final: 0.8288 (tptp)
REVERT: A  198 ILE cc_start: 0.9231 (OUTLIER) cc_final: 0.9011 (mp)
REVERT: A  247 LEU cc_start: 0.9076 (tp) cc_final: 0.8841 (tp)
REVERT: A  252 ARG cc_start: 0.8446 (mmm-85) cc_final: 0.8030 (mmt90)
REVERT: A  345 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8256 (mm-30)
REVERT: A  356 ARG cc_start: 0.7668 (mmt-90) cc_final: 0.6929 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8413 (pttp) cc_final: 0.8061 (mtmm)
REVERT: A  360 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7906 (mt-10)
REVERT: A  365 GLN cc_start: 0.8716 (tp40) cc_final: 0.8422 (tp40)
REVERT: A  383 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8698 (tm-30)
REVERT: C   80 LYS cc_start: 0.8473 (mtmm) cc_final: 0.7783 (mtmm)
REVERT: C   84 ASP cc_start: 0.8222 (m-30) cc_final: 0.7910 (m-30)
REVERT: C  250 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8661 (tt)
REVERT: C  255 LYS cc_start: 0.3081 (mmtt) cc_final: 0.2180 (mmtt)
REVERT: C  345 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8196 (mm-30)
REVERT: C  357 LYS cc_start: 0.8758 (mtmm) cc_final: 0.8335 (mtmm)
REVERT: C  365 GLN cc_start: 0.8909 (tp40) cc_final: 0.8513 (tp-100)
  outliers start: 32
  outliers final: 23
  residues processed: 337
  average time/residue: 0.1068
  time to fit residues: 48.0396
Evaluate side-chains
  335 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 310
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
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  211 TYR
Chi-restraints excluded: chain B residue  275 GLU
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  144 LEU
Chi-restraints excluded: chain A residue  197 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain C residue   30 ASN
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  209 ASP
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  319 VAL
Chi-restraints excluded: chain C residue  354 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 115 optimal weight:    6.9990
   chunk 110 optimal weight:    3.9990
   chunk 85 optimal weight:    9.9990
   chunk 44 optimal weight:    7.9990
   chunk 29 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 371 HIS
B 380 GLN
** A 293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  32 GLN
C 293 HIS
C 324 GLN
** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.177790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.151688 restraints weight = 19237.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 3.88
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4053
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4053 r_free = 0.4053    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4052 r_free = 0.4052    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (16 function evaluations)
r_final: 0.4052
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          1.1362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.139  10450  Z= 0.458
  Angle     :  1.636  47.931  14404  Z= 0.857
  Chirality :  0.208   4.757   1722
  Planarity :  0.008   0.161   1632
  Dihedral  : 21.378 177.701   1932
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 42.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 29.05 %
    Favored  : 68.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.25), residues: 1125
  helix:  0.13 (0.19), residues: 753
  sheet: -2.68 (0.76), residues: 30
  loop : -0.81 (0.37), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 188 
 TYR   0.031   0.003   TYR B  65 
 PHE   0.030   0.002   PHE A 184 
 TRP   0.004   0.001   TRP C 174 
 HIS   0.008   0.001   HIS B 331 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00806 /  0.46 (10450)
  covalent geometry    : angle       1.63600 /  0.86 (14404)
  hydrogen bonds       : bond        0.42562 / 27.76 (  651)
  hydrogen bonds       : angle       5.49775 /  3.90 ( 1719)

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

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 314
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   80 LYS cc_start: 0.8474 (mtmm) cc_final: 0.8192 (mtmm)
REVERT: B   88 GLU cc_start: 0.8174 (tp30) cc_final: 0.7965 (tp30)
REVERT: B  173 HIS cc_start: 0.7785 (t-90) cc_final: 0.7522 (t-90)
REVERT: B  180 MET cc_start: 0.8846 (mpp) cc_final: 0.8627 (mpp)
REVERT: B  252 ARG cc_start: 0.8135 (mmt90) cc_final: 0.7846 (mmt90)
REVERT: B  345 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8452 (mm-30)
REVERT: B  356 ARG cc_start: 0.7669 (mmt-90) cc_final: 0.7101 (mmt-90)
REVERT: B  365 GLN cc_start: 0.8752 (tp40) cc_final: 0.8543 (tp40)
REVERT: B  382 ARG cc_start: 0.8606 (mmp80) cc_final: 0.8325 (mmp-170)
REVERT: A    3 ASP cc_start: 0.8997 (t0) cc_final: 0.8696 (t0)
REVERT: A   44 ASN cc_start: 0.9228 (p0) cc_final: 0.8823 (p0)
REVERT: A   47 ILE cc_start: 0.9130 (mm) cc_final: 0.8870 (mp)
REVERT: A   65 TYR cc_start: 0.5799 (m-80) cc_final: 0.5559 (m-80)
REVERT: A   80 LYS cc_start: 0.8369 (mtmm) cc_final: 0.7908 (mtmm)
REVERT: A   81 TYR cc_start: 0.8348 (t80) cc_final: 0.8096 (t80)
REVERT: A   84 ASP cc_start: 0.8037 (m-30) cc_final: 0.7740 (m-30)
REVERT: A  163 GLN cc_start: 0.8406 (pt0) cc_final: 0.8051 (pp30)
REVERT: A  181 LYS cc_start: 0.8461 (tptt) cc_final: 0.8244 (tptp)
REVERT: A  198 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8999 (mp)
REVERT: A  252 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8029 (mmt90)
REVERT: A  345 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8306 (mm-30)
REVERT: A  356 ARG cc_start: 0.7641 (mmt-90) cc_final: 0.7215 (mmt-90)
REVERT: A  357 LYS cc_start: 0.8335 (pttp) cc_final: 0.8008 (mtmm)
REVERT: A  387 ARG cc_start: 0.8212 (tpp-160) cc_final: 0.7942 (tpm170)
REVERT: C    3 ASP cc_start: 0.8564 (t0) cc_final: 0.8281 (t0)
REVERT: C   47 ILE cc_start: 0.9193 (mm) cc_final: 0.8847 (mp)
REVERT: C   80 LYS cc_start: 0.8485 (mtmm) cc_final: 0.7805 (mtmm)
REVERT: C   84 ASP cc_start: 0.8223 (m-30) cc_final: 0.7900 (m-30)
REVERT: C  173 HIS cc_start: 0.7895 (t-90) cc_final: 0.7694 (t-90)
REVERT: C  180 MET cc_start: 0.8661 (mpp) cc_final: 0.8303 (mpp)
REVERT: C  250 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8732 (tt)
REVERT: C  255 LYS cc_start: 0.3194 (mmtt) cc_final: 0.2189 (mmtt)
REVERT: C  345 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8272 (mm-30)
REVERT: C  357 LYS cc_start: 0.8775 (mtmm) cc_final: 0.8544 (mtmm)
REVERT: C  365 GLN cc_start: 0.8901 (tp40) cc_final: 0.8515 (tp-100)
REVERT: C  382 ARG cc_start: 0.8656 (mmp80) cc_final: 0.8168 (mmp-170)
  outliers start: 24
  outliers final: 21
  residues processed: 324
  average time/residue: 0.0987
  time to fit residues: 42.6564
Evaluate side-chains
  326 residues out of total 981 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 303
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   23 LYS
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  275 GLU
Chi-restraints excluded: chain B residue  343 HIS
Chi-restraints excluded: chain B residue  374 THR
Chi-restraints excluded: chain A residue    9 GLU
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  141 LEU
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  230 VAL
Chi-restraints excluded: chain A residue  296 TYR
Chi-restraints excluded: chain A residue  374 THR
Chi-restraints excluded: chain C residue   30 ASN
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  250 LEU
Chi-restraints excluded: chain C residue  319 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 49 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 103 optimal weight:    0.0670
   chunk 113 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 86 optimal weight:    0.0010
   chunk 66 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0470
   overall best weight:    0.2822

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 344 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 324 GLN
C 341 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.183532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.156838 restraints weight = 19296.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.4108 rms_B_bonded: 4.06
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4110
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4110 r_free = 0.4110    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4110 r_free = 0.4110    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.4110
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          1.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.130  10450  Z= 0.439
  Angle     :  1.598  45.304  14404  Z= 0.829
  Chirality :  0.206   4.700   1722
  Planarity :  0.008   0.112   1632
  Dihedral  : 21.352 179.950   1932
  Min Nonbonded Distance : 1.854

Molprobity Statistics.
  All-atom Clashscore : 41.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 28.44 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.25), residues: 1125
  helix: -0.06 (0.19), residues: 762
  sheet: -2.88 (0.73), residues: 30
  loop : -0.74 (0.38), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 382 
 TYR   0.052   0.004   TYR A 211 
 PHE   0.026   0.002   PHE B 184 
 TRP   0.010   0.001   TRP C 174 
 HIS   0.007   0.001   HIS B 331 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00762 /  0.44 (10450)
  covalent geometry    : angle       1.59828 /  0.83 (14404)
  hydrogen bonds       : bond        0.42218 / 27.63 (  651)
  hydrogen bonds       : angle       5.57255 /  3.94 ( 1719)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2359.73 seconds
wall clock time: 41 minutes 28.19 seconds (2488.19 seconds total)