Starting phenix.real_space_refine
on Wed Sep 17 04:40:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wxe_37904/09_2025/8wxe_37904.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wxe_37904/09_2025/8wxe_37904.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wxe_37904/09_2025/8wxe_37904.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wxe_37904/09_2025/8wxe_37904.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wxe_37904/09_2025/8wxe_37904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wxe_37904/09_2025/8wxe_37904.map"
  }
  resolution = 4.0
  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=  -0.001 sd=   0.003
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: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    2865      2.51       5
     N     692      2.21       5
     O     794      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4388
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "a"
      Number of atoms: 226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 226
          Classifications: {'peptide': 28}
          Link IDs: {'PTRANS': 1, 'TRANS': 26}
    Chain: "b"
      Number of atoms: 226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 226
          Classifications: {'peptide': 28}
          Link IDs: {'PTRANS': 1, 'TRANS': 26}
    Chain: "d"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 817
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 3, 'TRANS': 101}
    Chain: "e"
      Number of atoms: 853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 853
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 4, 'TRANS': 101}
          Chain breaks: 2
    Chain: "f"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 847
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 3, 'TRANS': 102}
          Chain breaks: 2
    Chain: "g"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 821
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 2, 'TRANS': 101}
          Chain breaks: 2
    Chain: "m"
      Number of atoms: 268
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 268
          Classifications: {'peptide': 34}
          Link IDs: {'TRANS': 33}
    Chain: "n"
      Number of atoms: 302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 302
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
    Chain: "g"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.36, per 1000 atoms: 0.31
  Number of scatterers: 4388
  At special positions: 0
  Unit cell: (94.569, 82.612, 98.917, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O     794      8.00
     N     692      7.00
     C    2865      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS a  32 " - pdb=" SG  CYS b  32 " distance=2.03
    Simple disulfide: pdb=" SG  CYS d  37 " - pdb=" SG  CYS d  73 " distance=2.03
    Simple disulfide: pdb=" SG  CYS d  93 " - pdb=" SG  CYS d  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS e  49 " - pdb=" SG  CYS e  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS e 119 " - pdb=" SG  CYS e 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS f  49 " - pdb=" SG  CYS f  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS f 119 " - pdb=" SG  CYS f 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS g  46 " - pdb=" SG  CYS g  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS g 104 " - pdb=" SG  CYS g 107 " distance=2.04

  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: 0.28
  Conformation dependent library (CDL) restraints added in 169.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1028

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 9 sheets defined
      42.2% alpha, 13.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'a' and resid 27 through 54
      removed outlier: 4.323A  pdb=" N   LEU a  35 " --> pdb=" O   LEU a  31 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ASP a  36 " --> pdb=" O   CYS a  32 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ILE a  38 " --> pdb=" O   LEU a  34 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 28 through 54
    Processing helix  chain 'd' and resid 100 through 125
      removed outlier: 3.787A  pdb=" N   VAL d 104 " --> pdb=" O   ASP d 100 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR d 110 " --> pdb=" O   GLY d 106 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 126 through 152
      removed outlier: 3.706A  pdb=" N   VAL e 130 " --> pdb=" O   ASP e 126 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ILE e 133 " --> pdb=" O   SER e 129 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   VAL e 134 " --> pdb=" O   VAL e 130 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE e 135 " --> pdb=" O   ALA e 131 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 128 through 153
    Processing helix  chain 'g' and resid 111 through 140
      removed outlier: 4.749A  pdb=" N   GLY g 117 " --> pdb=" O   ALA g 113 " (cutoff:3.500A)
    Processing helix  chain 'm' and resid 258 through 288
      removed outlier: 3.667A  pdb=" N   PHE m 288 " --> pdb=" O   THR m 284 " (cutoff:3.500A)
    Processing helix  chain 'n' and resid 253 through 288
      removed outlier: 3.891A  pdb=" N   TYR n 264 " --> pdb=" O   THR n 260 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   MET n 265 " --> pdb=" O   SER n 261 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   VAL n 275 " --> pdb=" O   LEU n 271 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   TYR n 276 " --> pdb=" O   LYS n 272 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   CYS n 283 " --> pdb=" O   ILE n 279 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'd' and resid 33 through 36
      removed outlier: 7.108A  pdb=" N   VAL d  33 " --> pdb=" O   LEU d  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'd' and resid 41 through 46
      removed outlier: 3.668A  pdb=" N   VAL d  44 " --> pdb=" O   ILE d  70 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ILE d  70 " --> pdb=" O   VAL d  44 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   GLY d  46 " --> pdb=" O   ARG d  68 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   ARG d  68 " --> pdb=" O   GLY d  46 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY d  69 " --> pdb=" O   VAL d  88 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   VAL d  88 " --> pdb=" O   GLY d  69 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   TYR d  71 " --> pdb=" O   VAL d  86 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   VAL d  86 " --> pdb=" O   TYR d  71 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   THR d  85 " --> pdb=" O   TYR e 111 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   TYR e 113 " --> pdb=" O   THR d  85 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   GLN d  87 " --> pdb=" O   TYR e 113 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   ARG e 115 " --> pdb=" O   GLN d  87 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   HIS d  89 " --> pdb=" O   ARG e 115 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   PHE e 110 " --> pdb=" O   CYS e  98 " (cutoff:3.500A)
      removed outlier: 5.287A  pdb=" N   CYS e  98 " --> pdb=" O   PHE e 110 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   VAL e  97 " --> pdb=" O   GLN e  60 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   TYR e  99 " --> pdb=" O   LEU e  58 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'd' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'e' and resid 37 through 40
      removed outlier: 4.132A  pdb=" N   LYS e  37 " --> pdb=" O   THR e  48 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER e  83 " --> pdb=" O   GLY e  76 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   GLY e  76 " --> pdb=" O   SER e  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'f' and resid 45 through 47
      removed outlier: 3.536A  pdb=" N   LEU f  82 " --> pdb=" O   LEU f  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'f' and resid 122 through 123
      removed outlier: 3.588A  pdb=" N   MET f 123 " --> pdb=" O   ILE g 108 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'g' and resid 31 through 34
      removed outlier: 4.439A  pdb=" N   LEU g  43 " --> pdb=" O   TYR g  34 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLY g  75 " --> pdb=" O   VAL g  42 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   LEU g  44 " --> pdb=" O   ASN g  73 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   ASN g  73 " --> pdb=" O   LEU g  44 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'g' and resid 55 through 57
      removed outlier: 7.219A  pdb=" N   TRP g  55 " --> pdb=" O   ILE g  62 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   ILE g  62 " --> pdb=" O   TRP g  55 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'g' and resid 84 through 85
      removed outlier: 4.063A  pdb=" N   TYR g  85 " --> pdb=" O   LEU g  97 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   LEU g  97 " --> pdb=" O   TYR g  85 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    215 hydrogen bonds defined for protein.
    624 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.49

  Time building geometry restraints manager: 0.40 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1333
        1.34 -     1.47: 1083
        1.47 -     1.59: 2000
        1.59 -     1.71: 1
        1.71 -     1.83: 51
  Bond restraints: 4468
  Sorted by residual:
  bond pdb=" CB  PRO g  96 "
       pdb=" CG  PRO g  96 "
    ideal  model  delta    sigma   weight residual
    1.492  1.622 -0.130 5.00e-02 4.00e+02 6.72e+00
  bond pdb=" C   ASP a  28 "
       pdb=" N   PRO a  29 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.019 1.28e-02 6.10e+03 2.10e+00
  bond pdb=" N   PRO g  96 "
       pdb=" CA  PRO g  96 "
    ideal  model  delta    sigma   weight residual
    1.469  1.450  0.018 1.28e-02 6.10e+03 2.05e+00
  bond pdb=" CB  CYS a  32 "
       pdb=" SG  CYS a  32 "
    ideal  model  delta    sigma   weight residual
    1.808  1.772  0.036 3.30e-02 9.18e+02 1.17e+00
  bond pdb=" C3  CLR g 201 "
       pdb=" O1  CLR g 201 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.13e+00
  ... (remaining 4463 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.74: 5950
        2.74 -     5.48: 76
        5.48 -     8.22: 17
        8.22 -    10.96: 6
       10.96 -    13.70: 2
  Bond angle restraints: 6051
  Sorted by residual:
  angle pdb=" CA  PRO g  96 "
        pdb=" N   PRO g  96 "
        pdb=" CD  PRO g  96 "
      ideal   model   delta    sigma   weight residual
     112.00   98.30   13.70 1.40e+00 5.10e-01 9.58e+01
  angle pdb=" CA  GLU f 106 "
        pdb=" CB  GLU f 106 "
        pdb=" CG  GLU f 106 "
      ideal   model   delta    sigma   weight residual
     114.10  123.42   -9.32 2.00e+00 2.50e-01 2.17e+01
  angle pdb=" CB  MET f 123 "
        pdb=" CG  MET f 123 "
        pdb=" SD  MET f 123 "
      ideal   model   delta    sigma   weight residual
     112.70  124.29  -11.59 3.00e+00 1.11e-01 1.49e+01
  angle pdb=" N   PRO g  96 "
        pdb=" CD  PRO g  96 "
        pdb=" CG  PRO g  96 "
      ideal   model   delta    sigma   weight residual
     103.20   97.67    5.53 1.50e+00 4.44e-01 1.36e+01
  angle pdb=" N   PRO g  96 "
        pdb=" CA  PRO g  96 "
        pdb=" CB  PRO g  96 "
      ideal   model   delta    sigma   weight residual
     103.25   99.87    3.38 1.05e+00 9.07e-01 1.04e+01
  ... (remaining 6046 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 2228
       17.86 -    35.72: 372
       35.72 -    53.58: 94
       53.58 -    71.44: 20
       71.44 -    89.30: 4
  Dihedral angle restraints: 2718
    sinusoidal: 1122
      harmonic: 1596
  Sorted by residual:
  dihedral pdb=" CB  CYS a  32 "
           pdb=" SG  CYS a  32 "
           pdb=" SG  CYS b  32 "
           pdb=" CB  CYS b  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.21   72.21     1      1.00e+01 1.00e-02 6.67e+01
  dihedral pdb=" CB  CYS g 104 "
           pdb=" SG  CYS g 104 "
           pdb=" SG  CYS g 107 "
           pdb=" CB  CYS g 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.58   61.58     1      1.00e+01 1.00e-02 5.03e+01
  dihedral pdb=" CB  CYS d  37 "
           pdb=" SG  CYS d  37 "
           pdb=" SG  CYS d  73 "
           pdb=" CB  CYS d  73 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -132.94   46.94     1      1.00e+01 1.00e-02 3.05e+01
  ... (remaining 2715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 472
       0.034 -    0.068: 170
       0.068 -    0.102: 53
       0.102 -    0.136: 21
       0.136 -    0.170: 5
  Chirality restraints: 721
  Sorted by residual:
  chirality pdb=" CA  PRO f 105 "
            pdb=" N   PRO f 105 "
            pdb=" C   PRO f 105 "
            pdb=" CB  PRO f 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.25e-01
  chirality pdb=" C20 CLR g 201 "
            pdb=" C17 CLR g 201 "
            pdb=" C21 CLR g 201 "
            pdb=" C22 CLR g 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.43    0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  ASN g  28 "
            pdb=" N   ASN g  28 "
            pdb=" C   ASN g  28 "
            pdb=" CB  ASN g  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.44e-01
  ... (remaining 718 not shown)

  Planarity restraints: 728
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS g  95 "    0.119 5.00e-02 4.00e+02   1.68e-01 4.53e+01
        pdb=" N   PRO g  96 "   -0.290 5.00e-02 4.00e+02
        pdb=" CA  PRO g  96 "    0.090 5.00e-02 4.00e+02
        pdb=" CD  PRO g  96 "    0.081 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE d  24 "    0.037 5.00e-02 4.00e+02   5.62e-02 5.05e+00
        pdb=" N   PRO d  25 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO d  25 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO d  25 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU f  86 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.66e+00
        pdb=" CD  GLU f  86 "    0.037 2.00e-02 2.50e+03
        pdb=" OE1 GLU f  86 "   -0.014 2.00e-02 2.50e+03
        pdb=" OE2 GLU f  86 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 725 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 223
        2.72 -     3.27: 4463
        3.27 -     3.81: 7031
        3.81 -     4.36: 7314
        4.36 -     4.90: 12724
  Nonbonded interactions: 31755
  Sorted by model distance:
  nonbonded pdb=" O   SER f  41 "
            pdb=" OG1 THR f  44 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" NZ  LYS f 104 "
            pdb=" OE1 GLU f 106 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" O   GLN e  92 "
            pdb=" OH  TYR e  96 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" N   GLU e 124 "
            pdb=" OE1 GLU e 124 "
     model   vdw
     2.272 3.120
  nonbonded pdb=" OG  SER g 125 "
            pdb=" NZ  LYS n 272 "
     model   vdw
     2.321 3.120
  ... (remaining 31750 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'
}
ncs_group {
  reference = (chain 'e' and (resid 33 through 49 or resid 58 through 65 or resid 75 through 1 \ 
53))
  selection = (chain 'f' and (resid 33 through 65 or resid 75 through 101 or resid 109 through \ 
 153))
}

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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     5.860
  Find NCS groups from input model:        0.050
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
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      :  0.004   0.130   4477  Z= 0.171
  Angle     :  0.867  13.704   6069  Z= 0.453
  Chirality :  0.043   0.170    721
  Planarity :  0.008   0.168    728
  Dihedral  : 18.180  89.302   1663
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 19.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.96 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 40.73 %
    Favored  : 57.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.35), residues: 520
  helix:  1.55 (0.33), residues: 217
  sheet: -1.07 (0.61), residues: 71
  loop : -2.43 (0.35), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG e 115 
 TYR   0.023   0.001   TYR f  36 
 PHE   0.009   0.001   PHE f 110 
 TRP   0.025   0.002   TRP e  59 
 HIS   0.005   0.001   HIS g  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 4468)
  covalent geometry    : angle       0.86203 ( 6051)
  SS BOND              : bond        0.00235 (    9)
  SS BOND              : angle       1.90872 (   18)
  hydrogen bonds       : bond        0.18141 (  215)
  hydrogen bonds       : angle       6.34218 (  624)

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 214
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   52 ARG cc_start: 0.6571 (ttt180) cc_final: 0.6177 (ttt180)
REVERT: d   92 MET cc_start: 0.8431 (mtp) cc_final: 0.7777 (mmt)
REVERT: d   97 VAL cc_start: 0.8955 (t) cc_final: 0.8552 (p)
REVERT: d  109 VAL cc_start: 0.8934 (m) cc_final: 0.8674 (p)
REVERT: e   91 GLU cc_start: 0.9012 (pp20) cc_final: 0.8770 (pp20)
REVERT: e   92 GLN cc_start: 0.8518 (tt0) cc_final: 0.7882 (pt0)
REVERT: e   95 TYR cc_start: 0.6958 (m-80) cc_final: 0.6366 (m-10)
REVERT: e  145 LEU cc_start: 0.8539 (mm) cc_final: 0.8173 (tt)
REVERT: e  147 LEU cc_start: 0.8127 (tt) cc_final: 0.7906 (mm)
REVERT: f   97 VAL cc_start: 0.8610 (m) cc_final: 0.8234 (p)
REVERT: f  101 ARG cc_start: 0.7297 (mmt90) cc_final: 0.7068 (mpt180)
REVERT: f  121 ASN cc_start: 0.9297 (t0) cc_final: 0.8889 (t0)
REVERT: f  125 MET cc_start: 0.7019 (pmm) cc_final: 0.6524 (pmm)
REVERT: g   34 TYR cc_start: 0.8520 (t80) cc_final: 0.8285 (t80)
REVERT: g   39 ASP cc_start: 0.7355 (m-30) cc_final: 0.6312 (m-30)
REVERT: g   73 ASN cc_start: 0.9503 (t0) cc_final: 0.9216 (t0)
REVERT: g  103 MET cc_start: 0.7179 (mmp) cc_final: 0.6799 (mmp)
REVERT: g  119 LEU cc_start: 0.9204 (tp) cc_final: 0.8856 (tp)
REVERT: n  259 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7496 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 221
  average time/residue: 0.0700
  time to fit residues: 19.5725
Evaluate side-chains
  165 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 159
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   41 ILE
Chi-restraints excluded: chain a residue   42 TYR
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain d residue  124 CYS
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain n residue  259 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
d  89 HIS
e  92 GLN
g  86 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.142774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.110351 restraints weight = 10305.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.113782 restraints weight = 6910.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.114538 restraints weight = 4551.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.114593 restraints weight = 3654.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.114915 restraints weight = 3676.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   4477  Z= 0.168
  Angle     :  0.793   8.987   6069  Z= 0.397
  Chirality :  0.043   0.174    721
  Planarity :  0.005   0.090    728
  Dihedral  :  7.557  57.522    662
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 35.85 %
    Favored  : 57.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.34 (0.36), residues: 520
  helix:  2.06 (0.32), residues: 224
  sheet: -1.10 (0.58), residues: 77
  loop : -2.48 (0.35), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG n 287 
 TYR   0.016   0.001   TYR f 149 
 PHE   0.018   0.002   PHE g 127 
 TRP   0.010   0.002   TRP e  59 
 HIS   0.003   0.001   HIS d  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 4468)
  covalent geometry    : angle       0.78516 ( 6051)
  SS BOND              : bond        0.00373 (    9)
  SS BOND              : angle       2.16872 (   18)
  hydrogen bonds       : bond        0.04743 (  215)
  hydrogen bonds       : angle       4.57633 (  624)

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 175
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   46 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7296 (tt)
REVERT: a   52 ARG cc_start: 0.6616 (ttt180) cc_final: 0.6188 (ttt180)
REVERT: b   34 LEU cc_start: 0.7888 (tt) cc_final: 0.7177 (mm)
REVERT: d   72 ARG cc_start: 0.7801 (tpt-90) cc_final: 0.7318 (tpt-90)
REVERT: d   92 MET cc_start: 0.8145 (mtp) cc_final: 0.7517 (mmt)
REVERT: d   97 VAL cc_start: 0.8777 (t) cc_final: 0.8542 (p)
REVERT: d   98 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7771 (tm-30)
REVERT: d   99 LEU cc_start: 0.7325 (mp) cc_final: 0.7035 (mt)
REVERT: d  120 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8238 (tp)
REVERT: e   91 GLU cc_start: 0.8895 (pp20) cc_final: 0.8631 (pp20)
REVERT: e   92 GLN cc_start: 0.8650 (tt0) cc_final: 0.7917 (pt0)
REVERT: e  145 LEU cc_start: 0.8640 (mm) cc_final: 0.8058 (tt)
REVERT: e  147 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8034 (mm)
REVERT: f  104 LYS cc_start: 0.9133 (tmmt) cc_final: 0.8773 (ptmm)
REVERT: f  121 ASN cc_start: 0.9215 (t0) cc_final: 0.8886 (t0)
REVERT: g   34 TYR cc_start: 0.8699 (t80) cc_final: 0.8201 (t80)
REVERT: g   38 GLU cc_start: 0.7982 (pm20) cc_final: 0.7417 (pm20)
REVERT: g   44 LEU cc_start: 0.8601 (tt) cc_final: 0.7985 (tp)
REVERT: g   73 ASN cc_start: 0.9463 (t0) cc_final: 0.9208 (t0)
REVERT: g   82 ARG cc_start: 0.8682 (mmt90) cc_final: 0.8098 (mmt-90)
REVERT: g  119 LEU cc_start: 0.9070 (tp) cc_final: 0.8802 (tp)
REVERT: m  262 MET cc_start: 0.7549 (tpp) cc_final: 0.7013 (tpp)
REVERT: n  259 ASN cc_start: 0.7546 (OUTLIER) cc_final: 0.6618 (t0)
  outliers start: 32
  outliers final: 16
  residues processed: 191
  average time/residue: 0.0630
  time to fit residues: 15.2816
Evaluate side-chains
  185 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 165
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   34 LEU
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain b residue   39 LEU
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain d residue  124 CYS
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  129 SER
Chi-restraints excluded: chain e residue  147 LEU
Chi-restraints excluded: chain f residue   75 ILE
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  283 LEU
Chi-restraints excluded: chain n residue  259 ASN
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  280 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 31 optimal weight:   10.0000
   chunk 26 optimal weight:    0.0170
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
m 280 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.142729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.110863 restraints weight = 9954.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.114445 restraints weight = 6498.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.115283 restraints weight = 4161.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.115358 restraints weight = 3330.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.115732 restraints weight = 3467.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4477  Z= 0.141
  Angle     :  0.721   8.095   6069  Z= 0.361
  Chirality :  0.042   0.216    721
  Planarity :  0.004   0.062    728
  Dihedral  :  7.135  55.391    658
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  7.94 %
    Allowed  : 35.23 %
    Favored  : 56.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.35), residues: 520
  helix:  2.33 (0.32), residues: 222
  sheet: -0.54 (0.69), residues: 62
  loop : -2.47 (0.33), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG n 287 
 TYR   0.013   0.001   TYR e  36 
 PHE   0.029   0.002   PHE e 110 
 TRP   0.016   0.001   TRP e  59 
 HIS   0.001   0.001   HIS g  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4468)
  covalent geometry    : angle       0.71337 ( 6051)
  SS BOND              : bond        0.00327 (    9)
  SS BOND              : angle       2.06966 (   18)
  hydrogen bonds       : bond        0.04130 (  215)
  hydrogen bonds       : angle       4.17144 (  624)

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 168
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   46 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7240 (tt)
REVERT: a   52 ARG cc_start: 0.6525 (ttt180) cc_final: 0.6099 (ttt180)
REVERT: b   34 LEU cc_start: 0.7724 (tt) cc_final: 0.7109 (mm)
REVERT: d   63 ARG cc_start: 0.8877 (ttm170) cc_final: 0.8228 (mtp-110)
REVERT: d   72 ARG cc_start: 0.7778 (tpt-90) cc_final: 0.7481 (tpt-90)
REVERT: d   92 MET cc_start: 0.8107 (mtp) cc_final: 0.7419 (mmt)
REVERT: d   98 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7168 (tm-30)
REVERT: d  120 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8136 (tp)
REVERT: e   87 PHE cc_start: 0.8417 (OUTLIER) cc_final: 0.8192 (t80)
REVERT: e   91 GLU cc_start: 0.8973 (pp20) cc_final: 0.8723 (pp20)
REVERT: e   92 GLN cc_start: 0.8630 (tt0) cc_final: 0.7813 (pt0)
REVERT: e  145 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8203 (tt)
REVERT: f   38 VAL cc_start: 0.4673 (OUTLIER) cc_final: 0.4429 (p)
REVERT: f  104 LYS cc_start: 0.9236 (tmmt) cc_final: 0.8725 (tmmt)
REVERT: f  106 GLU cc_start: 0.8118 (mp0) cc_final: 0.7838 (mp0)
REVERT: f  117 ARG cc_start: 0.7891 (ptp90) cc_final: 0.7543 (ptt180)
REVERT: f  121 ASN cc_start: 0.9157 (t0) cc_final: 0.8748 (t0)
REVERT: f  125 MET cc_start: 0.6347 (pmm) cc_final: 0.5869 (pmm)
REVERT: g   34 TYR cc_start: 0.8529 (t80) cc_final: 0.8277 (t80)
REVERT: g   74 LEU cc_start: 0.8678 (tt) cc_final: 0.8318 (mt)
REVERT: g   82 ARG cc_start: 0.8589 (mmt90) cc_final: 0.8016 (mmt-90)
REVERT: g   84 MET cc_start: 0.5015 (mmm) cc_final: 0.4810 (mmm)
REVERT: g  119 LEU cc_start: 0.9025 (tp) cc_final: 0.8757 (tp)
REVERT: m  261 MET cc_start: 0.8292 (mmm) cc_final: 0.7922 (tpp)
REVERT: m  262 MET cc_start: 0.7573 (tpp) cc_final: 0.7075 (tpp)
REVERT: n  259 ASN cc_start: 0.7428 (OUTLIER) cc_final: 0.6618 (t0)
  outliers start: 39
  outliers final: 20
  residues processed: 191
  average time/residue: 0.0670
  time to fit residues: 16.2675
Evaluate side-chains
  178 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain b residue   39 LEU
Chi-restraints excluded: chain d residue   60 LEU
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain d residue  124 CYS
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   87 PHE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain f residue   38 VAL
Chi-restraints excluded: chain f residue   88 SER
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  126 ILE
Chi-restraints excluded: chain g residue  136 ILE
Chi-restraints excluded: chain m residue  256 THR
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  283 LEU
Chi-restraints excluded: chain n residue  259 ASN
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  280 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 23 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    0.1980
   chunk 3 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 49 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
e  60 GLN
f  61 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.141935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.111107 restraints weight = 9916.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.113765 restraints weight = 6891.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.114645 restraints weight = 4386.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.115649 restraints weight = 3182.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.116063 restraints weight = 2974.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.3872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4477  Z= 0.131
  Angle     :  0.707   9.006   6069  Z= 0.352
  Chirality :  0.042   0.167    721
  Planarity :  0.004   0.048    728
  Dihedral  :  7.035  54.218    658
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  8.76 %
    Allowed  : 34.22 %
    Favored  : 57.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.35), residues: 520
  helix:  2.29 (0.32), residues: 222
  sheet: -0.96 (0.63), residues: 71
  loop : -2.50 (0.33), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG f 115 
 TYR   0.016   0.001   TYR g  85 
 PHE   0.021   0.002   PHE a  40 
 TRP   0.016   0.001   TRP e  59 
 HIS   0.002   0.001   HIS f  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4468)
  covalent geometry    : angle       0.70237 ( 6051)
  SS BOND              : bond        0.00364 (    9)
  SS BOND              : angle       1.69914 (   18)
  hydrogen bonds       : bond        0.03768 (  215)
  hydrogen bonds       : angle       3.96972 (  624)

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 162
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   46 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7249 (tt)
REVERT: a   52 ARG cc_start: 0.6544 (ttt180) cc_final: 0.6144 (ttt180)
REVERT: d   63 ARG cc_start: 0.8895 (ttm170) cc_final: 0.8229 (mtp-110)
REVERT: d   92 MET cc_start: 0.8229 (mtp) cc_final: 0.7491 (mmt)
REVERT: d   98 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7743 (tm-30)
REVERT: d  120 LEU cc_start: 0.8400 (tt) cc_final: 0.8150 (tp)
REVERT: e   87 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8211 (t80)
REVERT: e  145 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8039 (tt)
REVERT: f   38 VAL cc_start: 0.4617 (OUTLIER) cc_final: 0.4369 (p)
REVERT: f   97 VAL cc_start: 0.9071 (m) cc_final: 0.8742 (p)
REVERT: f  104 LYS cc_start: 0.9299 (ttmt) cc_final: 0.8699 (tmmt)
REVERT: f  106 GLU cc_start: 0.8027 (mp0) cc_final: 0.7794 (mp0)
REVERT: f  120 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8660 (tm-30)
REVERT: f  121 ASN cc_start: 0.9160 (t0) cc_final: 0.8681 (t0)
REVERT: f  125 MET cc_start: 0.6647 (pmm) cc_final: 0.6243 (pmm)
REVERT: g   34 TYR cc_start: 0.8623 (t80) cc_final: 0.8365 (t80)
REVERT: g   38 GLU cc_start: 0.8457 (pm20) cc_final: 0.8240 (pm20)
REVERT: g   61 MET cc_start: 0.6615 (tpt) cc_final: 0.6038 (mmm)
REVERT: g  119 LEU cc_start: 0.9044 (tp) cc_final: 0.8765 (tp)
REVERT: m  261 MET cc_start: 0.8395 (mmm) cc_final: 0.8170 (mmm)
REVERT: n  259 ASN cc_start: 0.7475 (OUTLIER) cc_final: 0.6932 (t0)
  outliers start: 43
  outliers final: 26
  residues processed: 188
  average time/residue: 0.0692
  time to fit residues: 16.6665
Evaluate side-chains
  186 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 155
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain b residue   53 VAL
Chi-restraints excluded: chain d residue   60 LEU
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  116 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   87 PHE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  129 SER
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain f residue   38 VAL
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   88 SER
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  137 ASP
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  126 ILE
Chi-restraints excluded: chain g residue  136 ILE
Chi-restraints excluded: chain m residue  264 LEU
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  272 LEU
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  283 LEU
Chi-restraints excluded: chain n residue  257 LEU
Chi-restraints excluded: chain n residue  259 ASN
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  280 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 35 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 18 optimal weight:    7.9990
   chunk 9 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.141492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.109880 restraints weight = 10007.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.113940 restraints weight = 6677.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.114835 restraints weight = 3900.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.114909 restraints weight = 3089.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.115368 restraints weight = 3206.354|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7162
moved from start:          0.4076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4477  Z= 0.133
  Angle     :  0.728   8.131   6069  Z= 0.358
  Chirality :  0.042   0.156    721
  Planarity :  0.004   0.041    728
  Dihedral  :  6.631  53.406    655
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  9.57 %
    Allowed  : 35.64 %
    Favored  : 54.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.24 (0.35), residues: 520
  helix:  2.22 (0.33), residues: 222
  sheet: -1.01 (0.61), residues: 71
  loop : -2.47 (0.34), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG f 115 
 TYR   0.016   0.001   TYR g  85 
 PHE   0.019   0.001   PHE g 120 
 TRP   0.017   0.001   TRP e  59 
 HIS   0.001   0.001   HIS e  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4468)
  covalent geometry    : angle       0.72188 ( 6051)
  SS BOND              : bond        0.00257 (    9)
  SS BOND              : angle       1.91175 (   18)
  hydrogen bonds       : bond        0.03598 (  215)
  hydrogen bonds       : angle       3.91157 (  624)

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 158
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: a   30 LYS cc_start: 0.8305 (tmmt) cc_final: 0.8084 (mmtm)
REVERT: a   31 LEU cc_start: 0.8205 (pp) cc_final: 0.7755 (pp)
REVERT: a   46 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7209 (tt)
REVERT: a   52 ARG cc_start: 0.6640 (ttt180) cc_final: 0.6159 (ttt180)
REVERT: b   34 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7035 (mm)
REVERT: d   63 ARG cc_start: 0.8883 (ttm170) cc_final: 0.8279 (mtp-110)
REVERT: d   72 ARG cc_start: 0.7789 (tpt-90) cc_final: 0.7499 (tpp80)
REVERT: d   92 MET cc_start: 0.8274 (mtp) cc_final: 0.7539 (mmt)
REVERT: d   98 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7498 (tm-30)
REVERT: d  120 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8113 (tp)
REVERT: e   66 ILE cc_start: 0.6958 (OUTLIER) cc_final: 0.6654 (pt)
REVERT: e   92 GLN cc_start: 0.8388 (tt0) cc_final: 0.8058 (tt0)
REVERT: e  115 ARG cc_start: 0.8406 (ttm110) cc_final: 0.7820 (ttm110)
REVERT: e  120 GLU cc_start: 0.7485 (tm-30) cc_final: 0.7022 (tm-30)
REVERT: e  145 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8082 (tt)
REVERT: f   38 VAL cc_start: 0.4616 (OUTLIER) cc_final: 0.4377 (p)
REVERT: f  104 LYS cc_start: 0.9347 (ttmt) cc_final: 0.8455 (ttpp)
REVERT: f  120 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8613 (tm-30)
REVERT: f  121 ASN cc_start: 0.9159 (t0) cc_final: 0.8657 (t0)
REVERT: f  125 MET cc_start: 0.6610 (pmm) cc_final: 0.6037 (pmm)
REVERT: g   34 TYR cc_start: 0.8674 (t80) cc_final: 0.8410 (t80)
REVERT: g   61 MET cc_start: 0.6682 (tpt) cc_final: 0.5945 (mmm)
REVERT: g  119 LEU cc_start: 0.9040 (tp) cc_final: 0.8757 (tp)
REVERT: m  261 MET cc_start: 0.8420 (mmm) cc_final: 0.8155 (tpt)
REVERT: n  259 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.6886 (t0)
  outliers start: 47
  outliers final: 29
  residues processed: 186
  average time/residue: 0.0669
  time to fit residues: 15.8096
Evaluate side-chains
  186 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 150
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain b residue   53 VAL
Chi-restraints excluded: chain d residue   35 VAL
Chi-restraints excluded: chain d residue   60 LEU
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  116 LEU
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   66 ILE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  129 SER
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain f residue   38 VAL
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   46 ILE
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   88 SER
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain f residue  112 LEU
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  137 ASP
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  126 ILE
Chi-restraints excluded: chain g residue  136 ILE
Chi-restraints excluded: chain m residue  256 THR
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  276 THR
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  283 LEU
Chi-restraints excluded: chain n residue  259 ASN
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  280 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   chunk 42 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 41 optimal weight:    7.9990
   chunk 8 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.141265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.109192 restraints weight = 10144.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.112603 restraints weight = 6860.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.113560 restraints weight = 4276.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.113631 restraints weight = 3418.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.113979 restraints weight = 3623.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.4345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4477  Z= 0.141
  Angle     :  0.720   7.003   6069  Z= 0.358
  Chirality :  0.042   0.188    721
  Planarity :  0.004   0.036    728
  Dihedral  :  6.625  52.384    655
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  8.76 %
    Allowed  : 36.46 %
    Favored  : 54.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.35), residues: 520
  helix:  2.17 (0.33), residues: 225
  sheet: -1.08 (0.61), residues: 71
  loop : -2.54 (0.33), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG g  82 
 TYR   0.014   0.001   TYR g  85 
 PHE   0.025   0.002   PHE a  40 
 TRP   0.018   0.002   TRP e  59 
 HIS   0.001   0.001   HIS d  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4468)
  covalent geometry    : angle       0.71558 ( 6051)
  SS BOND              : bond        0.00331 (    9)
  SS BOND              : angle       1.67811 (   18)
  hydrogen bonds       : bond        0.03648 (  215)
  hydrogen bonds       : angle       3.86780 (  624)

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 155
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   30 LYS cc_start: 0.8334 (tmmt) cc_final: 0.8103 (mmtm)
REVERT: a   31 LEU cc_start: 0.8214 (pp) cc_final: 0.7771 (pp)
REVERT: a   46 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7271 (tt)
REVERT: a   52 ARG cc_start: 0.6596 (ttt180) cc_final: 0.6120 (ttt180)
REVERT: b   34 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7087 (mm)
REVERT: d   59 ASP cc_start: 0.7795 (p0) cc_final: 0.6869 (t0)
REVERT: d   63 ARG cc_start: 0.8916 (ttm170) cc_final: 0.8299 (mtp-110)
REVERT: d   92 MET cc_start: 0.8176 (mtp) cc_final: 0.7527 (mmt)
REVERT: d   98 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7449 (tm-30)
REVERT: d  120 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8096 (tp)
REVERT: e   92 GLN cc_start: 0.8301 (tt0) cc_final: 0.7951 (tt0)
REVERT: e  115 ARG cc_start: 0.8418 (ttm110) cc_final: 0.7770 (ttm110)
REVERT: e  145 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8108 (tt)
REVERT: f  104 LYS cc_start: 0.9309 (ttmt) cc_final: 0.9002 (ttpp)
REVERT: f  120 GLU cc_start: 0.8991 (tm-30) cc_final: 0.8606 (tm-30)
REVERT: f  121 ASN cc_start: 0.9149 (t0) cc_final: 0.8571 (t0)
REVERT: f  125 MET cc_start: 0.6717 (pmm) cc_final: 0.6098 (pmm)
REVERT: g   34 TYR cc_start: 0.8692 (t80) cc_final: 0.8375 (t80)
REVERT: g  119 LEU cc_start: 0.8997 (tp) cc_final: 0.8706 (tp)
REVERT: g  129 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8275 (mt)
REVERT: m  257 GLU cc_start: 0.8235 (mp0) cc_final: 0.7953 (mp0)
REVERT: m  258 LYS cc_start: 0.8727 (mmtm) cc_final: 0.8522 (mmmm)
REVERT: m  261 MET cc_start: 0.8530 (mmm) cc_final: 0.8131 (tpt)
REVERT: m  271 MET cc_start: 0.8741 (tpp) cc_final: 0.8345 (tpp)
REVERT: n  259 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.6988 (t0)
  outliers start: 43
  outliers final: 32
  residues processed: 181
  average time/residue: 0.0711
  time to fit residues: 16.3442
Evaluate side-chains
  183 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 145
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   46 LEU
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain b residue   53 VAL
Chi-restraints excluded: chain d residue   35 VAL
Chi-restraints excluded: chain d residue   42 THR
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue   96 CYS
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  116 LEU
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  129 SER
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   46 ILE
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   88 SER
Chi-restraints excluded: chain f residue   90 LEU
Chi-restraints excluded: chain f residue  112 LEU
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  137 ASP
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  126 ILE
Chi-restraints excluded: chain g residue  129 LEU
Chi-restraints excluded: chain g residue  136 ILE
Chi-restraints excluded: chain m residue  256 THR
Chi-restraints excluded: chain m residue  264 LEU
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  276 THR
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  283 LEU
Chi-restraints excluded: chain n residue  257 LEU
Chi-restraints excluded: chain n residue  259 ASN
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  280 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 34 optimal weight:    8.9990
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
e 109 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.130191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.098083 restraints weight = 10029.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.101200 restraints weight = 7001.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.101827 restraints weight = 4809.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.101830 restraints weight = 3830.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.102146 restraints weight = 3876.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.5166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046   4477  Z= 0.308
  Angle     :  0.935   9.477   6069  Z= 0.469
  Chirality :  0.049   0.218    721
  Planarity :  0.005   0.038    728
  Dihedral  :  7.100  52.528    655
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers : 11.61 %
    Allowed  : 35.44 %
    Favored  : 52.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.34), residues: 520
  helix:  1.49 (0.31), residues: 224
  sheet: -1.25 (0.57), residues: 85
  loop : -2.61 (0.33), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG g  82 
 TYR   0.034   0.003   TYR f 149 
 PHE   0.022   0.003   PHE g 120 
 TRP   0.021   0.003   TRP g  55 
 HIS   0.011   0.003   HIS f  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00699 ( 4468)
  covalent geometry    : angle       0.92709 ( 6051)
  SS BOND              : bond        0.00459 (    9)
  SS BOND              : angle       2.42513 (   18)
  hydrogen bonds       : bond        0.05666 (  215)
  hydrogen bonds       : angle       4.59848 (  624)

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 155
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   42 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.6600 (t80)
REVERT: a   52 ARG cc_start: 0.6724 (ttt180) cc_final: 0.6084 (ttt180)
REVERT: b   34 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7449 (mm)
REVERT: d   62 LYS cc_start: 0.8657 (ptpp) cc_final: 0.7851 (mmpt)
REVERT: d   63 ARG cc_start: 0.9047 (ttm170) cc_final: 0.8287 (mtp-110)
REVERT: d   72 ARG cc_start: 0.7636 (tpp80) cc_final: 0.7374 (tpp80)
REVERT: d   92 MET cc_start: 0.8265 (mtp) cc_final: 0.7817 (mmt)
REVERT: d   98 GLU cc_start: 0.8204 (tm-30) cc_final: 0.6795 (tm-30)
REVERT: d  120 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8471 (tp)
REVERT: e  145 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8275 (tt)
REVERT: e  150 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7700 (m-10)
REVERT: f   59 TRP cc_start: 0.7968 (m100) cc_final: 0.7553 (m100)
REVERT: f  104 LYS cc_start: 0.9394 (ttmt) cc_final: 0.9100 (ttpp)
REVERT: f  121 ASN cc_start: 0.9095 (t0) cc_final: 0.8349 (t0)
REVERT: f  125 MET cc_start: 0.7833 (pmm) cc_final: 0.7067 (pmm)
REVERT: g   34 TYR cc_start: 0.8704 (t80) cc_final: 0.8368 (t80)
REVERT: g   61 MET cc_start: 0.6248 (tpt) cc_final: 0.5933 (tpt)
REVERT: g  111 ASN cc_start: 0.8895 (OUTLIER) cc_final: 0.8583 (p0)
REVERT: m  261 MET cc_start: 0.8834 (mmm) cc_final: 0.8392 (tpt)
REVERT: n  259 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7506 (t0)
  outliers start: 57
  outliers final: 30
  residues processed: 190
  average time/residue: 0.0672
  time to fit residues: 16.4000
Evaluate side-chains
  186 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 149
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   34 LEU
Chi-restraints excluded: chain a residue   42 TYR
Chi-restraints excluded: chain a residue   53 VAL
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain b residue   41 ILE
Chi-restraints excluded: chain d residue   35 VAL
Chi-restraints excluded: chain d residue   42 THR
Chi-restraints excluded: chain d residue   66 ASP
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue   96 CYS
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain e residue   34 THR
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   66 ILE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  129 SER
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain e residue  150 TYR
Chi-restraints excluded: chain f residue   40 ILE
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  137 ASP
Chi-restraints excluded: chain f residue  147 LEU
Chi-restraints excluded: chain g residue   88 LYS
Chi-restraints excluded: chain g residue   97 LEU
Chi-restraints excluded: chain g residue  111 ASN
Chi-restraints excluded: chain g residue  126 ILE
Chi-restraints excluded: chain m residue  256 THR
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  276 THR
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  283 LEU
Chi-restraints excluded: chain n residue  259 ASN
Chi-restraints excluded: chain n residue  274 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 15 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 6 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.136005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.104060 restraints weight = 9711.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.107679 restraints weight = 6589.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.108452 restraints weight = 4233.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.108402 restraints weight = 3352.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.108729 restraints weight = 3534.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7282
moved from start:          0.5240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4477  Z= 0.157
  Angle     :  0.836  11.080   6069  Z= 0.406
  Chirality :  0.045   0.171    721
  Planarity :  0.004   0.028    728
  Dihedral  :  7.121  54.789    655
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 42.57 %
    Favored  : 51.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.35), residues: 520
  helix:  1.93 (0.32), residues: 224
  sheet: -1.00 (0.58), residues: 85
  loop : -2.59 (0.32), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG f 115 
 TYR   0.018   0.001   TYR g 100 
 PHE   0.029   0.002   PHE a  40 
 TRP   0.019   0.002   TRP e  59 
 HIS   0.003   0.001   HIS f  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 4468)
  covalent geometry    : angle       0.83012 ( 6051)
  SS BOND              : bond        0.00295 (    9)
  SS BOND              : angle       1.97413 (   18)
  hydrogen bonds       : bond        0.04403 (  215)
  hydrogen bonds       : angle       4.01692 (  624)

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 160
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   42 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.6547 (t80)
REVERT: a   52 ARG cc_start: 0.6701 (ttt180) cc_final: 0.5954 (ttt180)
REVERT: b   34 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7198 (mm)
REVERT: b   42 TYR cc_start: 0.7460 (t80) cc_final: 0.7249 (t80)
REVERT: d   63 ARG cc_start: 0.9004 (ttm170) cc_final: 0.8250 (mtp-110)
REVERT: d   72 ARG cc_start: 0.7585 (tpp80) cc_final: 0.7316 (tpp80)
REVERT: d   92 MET cc_start: 0.8287 (mtp) cc_final: 0.7778 (mmt)
REVERT: d   98 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7269 (tm-30)
REVERT: d  120 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8302 (tp)
REVERT: e   87 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.8040 (t80)
REVERT: e  115 ARG cc_start: 0.8480 (ttm110) cc_final: 0.8172 (ttm110)
REVERT: e  145 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8291 (tt)
REVERT: f   59 TRP cc_start: 0.7556 (m100) cc_final: 0.6919 (m100)
REVERT: f  104 LYS cc_start: 0.9400 (ttmt) cc_final: 0.9032 (ttpp)
REVERT: f  110 PHE cc_start: 0.7400 (p90) cc_final: 0.7062 (p90)
REVERT: f  120 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8631 (tm-30)
REVERT: f  121 ASN cc_start: 0.9153 (t0) cc_final: 0.8368 (t0)
REVERT: f  125 MET cc_start: 0.7403 (pmm) cc_final: 0.6633 (pmm)
REVERT: g   34 TYR cc_start: 0.8787 (t80) cc_final: 0.8452 (t80)
REVERT: g  129 LEU cc_start: 0.8381 (mp) cc_final: 0.7997 (mt)
REVERT: m  257 GLU cc_start: 0.8101 (mp0) cc_final: 0.7758 (mp0)
REVERT: m  258 LYS cc_start: 0.8776 (mmtm) cc_final: 0.8513 (mmmm)
REVERT: m  261 MET cc_start: 0.8684 (mmm) cc_final: 0.8207 (tpt)
REVERT: n  259 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7274 (t0)
  outliers start: 29
  outliers final: 20
  residues processed: 174
  average time/residue: 0.0725
  time to fit residues: 16.0446
Evaluate side-chains
  177 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 151
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   42 TYR
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain d residue   35 VAL
Chi-restraints excluded: chain d residue   42 THR
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue   96 CYS
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  116 LEU
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   87 PHE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue   97 VAL
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  137 ASP
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  147 LEU
Chi-restraints excluded: chain g residue  126 ILE
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  286 LYS
Chi-restraints excluded: chain n residue  257 LEU
Chi-restraints excluded: chain n residue  259 ASN
Chi-restraints excluded: chain n residue  274 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 17 optimal weight:   10.0000
   chunk 38 optimal weight:    0.0980
   chunk 29 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 10 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 22 optimal weight:    0.1980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
** f  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.138683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.106594 restraints weight = 9562.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.110282 restraints weight = 6427.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.111286 restraints weight = 3980.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.111182 restraints weight = 3162.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.111581 restraints weight = 3348.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.5364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4477  Z= 0.153
  Angle     :  0.845  12.352   6069  Z= 0.409
  Chirality :  0.045   0.161    721
  Planarity :  0.004   0.029    728
  Dihedral  :  6.952  54.364    655
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  5.91 %
    Allowed  : 43.58 %
    Favored  : 50.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.35), residues: 520
  helix:  2.08 (0.33), residues: 221
  sheet: -0.89 (0.59), residues: 85
  loop : -2.64 (0.32), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG g  82 
 TYR   0.013   0.001   TYR g 101 
 PHE   0.025   0.002   PHE g 120 
 TRP   0.020   0.002   TRP e  59 
 HIS   0.007   0.001   HIS f  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4468)
  covalent geometry    : angle       0.83846 ( 6051)
  SS BOND              : bond        0.00279 (    9)
  SS BOND              : angle       2.13435 (   18)
  hydrogen bonds       : bond        0.03895 (  215)
  hydrogen bonds       : angle       3.86501 (  624)

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: a   42 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6650 (t80)
REVERT: a   52 ARG cc_start: 0.6498 (ttt180) cc_final: 0.5835 (ttt180)
REVERT: b   34 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7174 (mm)
REVERT: b   42 TYR cc_start: 0.7489 (t80) cc_final: 0.7266 (t80)
REVERT: d   63 ARG cc_start: 0.8998 (ttm170) cc_final: 0.8274 (mtp-110)
REVERT: d   72 ARG cc_start: 0.7634 (tpp80) cc_final: 0.7349 (tpp80)
REVERT: d   92 MET cc_start: 0.8232 (mtp) cc_final: 0.7736 (mmt)
REVERT: d   98 GLU cc_start: 0.8114 (tm-30) cc_final: 0.6688 (tm-30)
REVERT: d  120 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8229 (tp)
REVERT: e   87 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.8277 (t80)
REVERT: e  115 ARG cc_start: 0.8475 (ttm110) cc_final: 0.8141 (ttm110)
REVERT: e  145 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8324 (tt)
REVERT: f  104 LYS cc_start: 0.9337 (ttmt) cc_final: 0.9010 (ttpp)
REVERT: f  110 PHE cc_start: 0.7559 (p90) cc_final: 0.7240 (p90)
REVERT: f  121 ASN cc_start: 0.9115 (t0) cc_final: 0.8406 (t0)
REVERT: f  125 MET cc_start: 0.7214 (pmm) cc_final: 0.6459 (pmm)
REVERT: g   34 TYR cc_start: 0.8717 (t80) cc_final: 0.8444 (t80)
REVERT: m  257 GLU cc_start: 0.8112 (mp0) cc_final: 0.7781 (mp0)
REVERT: m  258 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8454 (mmmt)
REVERT: m  261 MET cc_start: 0.8655 (mmm) cc_final: 0.8225 (tpt)
REVERT: n  259 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7043 (t0)
  outliers start: 29
  outliers final: 17
  residues processed: 172
  average time/residue: 0.0742
  time to fit residues: 16.1897
Evaluate side-chains
  177 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   42 TYR
Chi-restraints excluded: chain b residue   34 LEU
Chi-restraints excluded: chain d residue   35 VAL
Chi-restraints excluded: chain d residue   42 THR
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   87 PHE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue  118 VAL
Chi-restraints excluded: chain f residue  137 ASP
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  147 LEU
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  286 LYS
Chi-restraints excluded: chain n residue  257 LEU
Chi-restraints excluded: chain n residue  259 ASN
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  280 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0020
   chunk 45 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.7590

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

Flipped N/Q/H residues before XYZ refinement:
** f  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.139179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.107322 restraints weight = 9543.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.110980 restraints weight = 6235.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.111969 restraints weight = 3889.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.111941 restraints weight = 3071.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.112198 restraints weight = 3314.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.5524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4477  Z= 0.151
  Angle     :  0.830  11.338   6069  Z= 0.405
  Chirality :  0.043   0.159    721
  Planarity :  0.004   0.031    728
  Dihedral  :  6.819  51.870    655
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 44.20 %
    Favored  : 50.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.31 (0.35), residues: 520
  helix:  2.16 (0.33), residues: 221
  sheet: -0.81 (0.63), residues: 71
  loop : -2.58 (0.31), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG g  82 
 TYR   0.020   0.001   TYR n 276 
 PHE   0.028   0.002   PHE e 110 
 TRP   0.016   0.002   TRP e  59 
 HIS   0.003   0.001   HIS f  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4468)
  covalent geometry    : angle       0.82462 ( 6051)
  SS BOND              : bond        0.00301 (    9)
  SS BOND              : angle       1.94955 (   18)
  hydrogen bonds       : bond        0.03809 (  215)
  hydrogen bonds       : angle       3.81017 (  624)

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

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

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1040 Ramachandran restraints generated.
    520 Oldfield, 0 Emsley, 520 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 154
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: a   42 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.6177 (t80)
REVERT: a   52 ARG cc_start: 0.6529 (ttt180) cc_final: 0.5847 (ttt180)
REVERT: b   40 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7813 (t80)
REVERT: d   63 ARG cc_start: 0.8982 (ttm170) cc_final: 0.8248 (mtp-110)
REVERT: d   92 MET cc_start: 0.8259 (mtp) cc_final: 0.7735 (mmt)
REVERT: d   98 GLU cc_start: 0.7958 (tm-30) cc_final: 0.7279 (tm-30)
REVERT: d  120 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8140 (tp)
REVERT: e   87 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8233 (t80)
REVERT: e  115 ARG cc_start: 0.8484 (ttm110) cc_final: 0.8034 (ttm110)
REVERT: e  145 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8213 (tt)
REVERT: f  104 LYS cc_start: 0.9317 (ttmt) cc_final: 0.9022 (ttpp)
REVERT: f  110 PHE cc_start: 0.7599 (p90) cc_final: 0.7282 (p90)
REVERT: f  121 ASN cc_start: 0.9184 (t0) cc_final: 0.8116 (t0)
REVERT: f  125 MET cc_start: 0.7016 (pmm) cc_final: 0.6265 (pmm)
REVERT: g   34 TYR cc_start: 0.8707 (t80) cc_final: 0.8434 (t80)
REVERT: m  257 GLU cc_start: 0.8230 (mp0) cc_final: 0.7977 (mp0)
REVERT: m  258 LYS cc_start: 0.8707 (mmtm) cc_final: 0.8465 (mmmt)
REVERT: m  261 MET cc_start: 0.8616 (mmm) cc_final: 0.8180 (tpt)
REVERT: n  259 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7059 (t0)
  outliers start: 25
  outliers final: 18
  residues processed: 166
  average time/residue: 0.0749
  time to fit residues: 15.7445
Evaluate side-chains
  172 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 148
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain a residue   42 TYR
Chi-restraints excluded: chain b residue   40 PHE
Chi-restraints excluded: chain b residue   49 LEU
Chi-restraints excluded: chain d residue   35 VAL
Chi-restraints excluded: chain d residue   42 THR
Chi-restraints excluded: chain d residue   88 VAL
Chi-restraints excluded: chain d residue  112 VAL
Chi-restraints excluded: chain d residue  120 LEU
Chi-restraints excluded: chain e residue   38 VAL
Chi-restraints excluded: chain e residue   87 PHE
Chi-restraints excluded: chain e residue  114 LEU
Chi-restraints excluded: chain e residue  145 LEU
Chi-restraints excluded: chain f residue   84 LEU
Chi-restraints excluded: chain f residue  137 ASP
Chi-restraints excluded: chain f residue  138 ILE
Chi-restraints excluded: chain f residue  147 LEU
Chi-restraints excluded: chain m residue  266 VAL
Chi-restraints excluded: chain m residue  277 VAL
Chi-restraints excluded: chain m residue  279 VAL
Chi-restraints excluded: chain m residue  286 LYS
Chi-restraints excluded: chain n residue  257 LEU
Chi-restraints excluded: chain n residue  259 ASN
Chi-restraints excluded: chain n residue  274 VAL
Chi-restraints excluded: chain n residue  280 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 21 optimal weight:    7.9990
   chunk 2 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** f  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.137907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.107100 restraints weight = 9993.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.110388 restraints weight = 6787.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.110968 restraints weight = 4074.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.111417 restraints weight = 3083.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.111777 restraints weight = 3039.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7249
moved from start:          0.5652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4477  Z= 0.162
  Angle     :  0.884  12.627   6069  Z= 0.425
  Chirality :  0.045   0.209    721
  Planarity :  0.003   0.031    728
  Dihedral  :  6.707  50.129    655
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 44.40 %
    Favored  : 50.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.35), residues: 520
  helix:  2.25 (0.33), residues: 220
  sheet: -0.84 (0.58), residues: 83
  loop : -2.63 (0.32), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG f 115 
 TYR   0.018   0.001   TYR g  85 
 PHE   0.026   0.002   PHE g 120 
 TRP   0.014   0.002   TRP e  59 
 HIS   0.004   0.001   HIS e  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 4468)
  covalent geometry    : angle       0.87723 ( 6051)
  SS BOND              : bond        0.00266 (    9)
  SS BOND              : angle       2.12085 (   18)
  hydrogen bonds       : bond        0.03749 (  215)
  hydrogen bonds       : angle       3.82557 (  624)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 993.17 seconds
wall clock time: 17 minutes 51.99 seconds (1071.99 seconds total)