Starting phenix.real_space_refine
on Sun Aug 24 07:05:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c9a_16507/08_2025/8c9a_16507.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c9a_16507/08_2025/8c9a_16507.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c9a_16507/08_2025/8c9a_16507.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c9a_16507/08_2025/8c9a_16507.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c9a_16507/08_2025/8c9a_16507.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c9a_16507/08_2025/8c9a_16507.cif"
  }
  resolution = 4.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     650      5.49       5
     S      10      5.16       5
     C    8805      2.51       5
     N    3358      2.21       5
     O    5236      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18059
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 13953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 650, 13953
          Classifications: {'RNA': 650}
          Modifications used: {'rna2p_pur': 70, 'rna2p_pyr': 42, 'rna3p_pur': 314, 'rna3p_pyr': 224}
          Link IDs: {'rna2p': 112, 'rna3p': 537}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'  U%rna2p_pyr:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "2"
      Number of atoms: 286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 286
          Classifications: {'peptide': 35}
          Link IDs: {'TRANS': 34}
    Chain: "E"
      Number of atoms: 1137
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1137
          Classifications: {'peptide': 147}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 144}
          Chain breaks: 1
    Chain: "S"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 726
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 92}
          Chain breaks: 1
    Chain: "U"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 779
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 3, 'TRANS': 98}
    Chain: "Y"
      Number of atoms: 494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 60, 494
          Classifications: {'peptide': 60}
          Link IDs: {'TRANS': 59}
    Chain: "T"
      Number of atoms: 684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 684
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
          Chain breaks: 1
  Time building chain proxies: 4.46, per 1000 atoms: 0.25
  Number of scatterers: 18059
  At special positions: 0
  Unit cell: (132.5, 152.5, 148.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     650     15.00
     O    5236      8.00
     N    3358      7.00
     C    8805      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.54
  Conformation dependent library (CDL) restraints added in 304.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  998

  Finding SS restraints...
Warning! N1 atom is missing from residue    G A 356  
  Was trying to link:    G A 356 N1 with    U A 284 O4, Saenger class: 27
Warning! N1 atom is missing from residue    G A 356  
  Was trying to link:    G A 356 N1 with    U A 284 O2, Saenger class: 28
    Secondary structure from input PDB file:
      19 helices and 5 sheets defined
      44.6% alpha, 14.7% beta
      198 base pairs and 310 stacking pairs defined.
    Time for finding SS restraints: 3.02
  Creating SS restraints...
    Processing helix  chain '2' and resid 10 through 17
    Processing helix  chain '2' and resid 17 through 24
      removed outlier: 4.282A  pdb=" N   THR 2  24 " --> pdb=" O   ALA 2  20 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 24 through 38
    Processing helix  chain 'E' and resid 15 through 20
    Processing helix  chain 'E' and resid 24 through 38
    Processing helix  chain 'E' and resid 97 through 115
    Processing helix  chain 'E' and resid 130 through 141
      removed outlier: 3.689A  pdb=" N   LEU E 134 " --> pdb=" O   LYS E 130 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   MET E 141 " --> pdb=" O   LYS E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 154 through 162
    Processing helix  chain 'E' and resid 176 through 183
      removed outlier: 3.566A  pdb=" N   PHE E 183 " --> pdb=" O   SER E 179 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 201
    Processing helix  chain 'S' and resid 13 through 22
    Processing helix  chain 'S' and resid 28 through 38
      removed outlier: 4.349A  pdb=" N   TYR S  38 " --> pdb=" O   ASP S  34 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 41 through 63
      removed outlier: 3.789A  pdb=" N   VAL S  45 " --> pdb=" O   LYS S  41 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU S  46 " --> pdb=" O   LYS S  42 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 65 through 67
      No H-bonds generated for 'chain 'U' and resid 65 through 67'
    Processing helix  chain 'Y' and resid 9 through 35
      removed outlier: 3.525A  pdb=" N   GLU Y  13 " --> pdb=" O   LYS Y   9 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLN Y  25 " --> pdb=" O   LEU Y  21 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   PHE Y  26 " --> pdb=" O   LEU Y  22 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 40 through 56
      removed outlier: 3.817A  pdb=" N   LYS Y  44 " --> pdb=" O   SER Y  40 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU Y  56 " --> pdb=" O   ARG Y  52 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 4 through 9
      removed outlier: 3.531A  pdb=" N   LEU T   8 " --> pdb=" O   GLU T   4 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 17 through 27
      removed outlier: 3.847A  pdb=" N   GLU T  25 " --> pdb=" O   SER T  21 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 39 through 52
    Processing sheet with id=AA1, first strand: chain 'E' and resid 118 through 121
      removed outlier: 4.005A  pdb=" N   THR E 189 " --> pdb=" O   ILE E 149 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASP E 168 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'S' and resid 3 through 10
      removed outlier: 5.340A  pdb=" N   ILE S   4 " --> pdb=" O   VAL S 107 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   VAL S 107 " --> pdb=" O   ILE S   4 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   LYS S   6 " --> pdb=" O   VAL S 105 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   VAL S 105 " --> pdb=" O   LYS S   6 " (cutoff:3.500A)
      removed outlier: 5.440A  pdb=" N   ARG S   8 " --> pdb=" O   ILE S 103 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ILE S 103 " --> pdb=" O   ARG S   8 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   SER S 108 " --> pdb=" O   VAL S  71 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   VAL S  71 " --> pdb=" O   SER S 108 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'U' and resid 33 through 35
      removed outlier: 7.123A  pdb=" N   ILE U  34 " --> pdb=" O   LYS U  25 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ASP U   8 " --> pdb=" O   VAL U  24 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'U' and resid 83 through 86
    Processing sheet with id=AA5, first strand: chain 'T' and resid 29 through 34
      removed outlier: 3.604A  pdb=" N   ALA T  83 " --> pdb=" O   LEU T  32 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL T  34 " --> pdb=" O   LYS T  81 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   LYS T  81 " --> pdb=" O   VAL T  34 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR T  86 " --> pdb=" O   VAL T  57 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   VAL T  57 " --> pdb=" O   THR T  86 " (cutoff:3.500A)

    181 hydrogen bonds defined for protein.
    534 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      506 hydrogen bonds
      816 hydrogen bond angles
      0 basepair planarities
      198 basepair parallelities
      310 stacking parallelities
  Total time for adding SS restraints: 4.52

  Time building geometry restraints manager: 2.13 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2914
        1.33 -     1.45: 8282
        1.45 -     1.57: 7252
        1.57 -     1.69: 1294
        1.69 -     1.81: 20
  Bond restraints: 19762
  Sorted by residual:
  bond pdb=" N   ALA U   1 "
       pdb=" CA  ALA U   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.07e+00
  bond pdb=" N   MET Y   1 "
       pdb=" CA  MET Y   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.88e+00
  bond pdb=" N   MET T   1 "
       pdb=" CA  MET T   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.84e+00
  bond pdb=" C5    G A 356 "
       pdb=" C4    G A 356 "
    ideal  model  delta    sigma   weight residual
    1.379  1.397 -0.018 2.00e-02 2.50e+03 8.39e-01
  bond pdb=" C5    A A 278 "
       pdb=" C6    A A 278 "
    ideal  model  delta    sigma   weight residual
    1.406  1.422 -0.016 2.00e-02 2.50e+03 6.21e-01
  ... (remaining 19757 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.34: 29883
        5.34 -    10.68: 9
       10.68 -    16.03: 0
       16.03 -    21.37: 0
       21.37 -    26.71: 2
  Bond angle restraints: 29894
  Sorted by residual:
  angle pdb=" O3'   C A 624 "
        pdb=" P     G A 625 "
        pdb=" OP1   G A 625 "
      ideal   model   delta    sigma   weight residual
     108.00   81.29   26.71 3.00e+00 1.11e-01 7.93e+01
  angle pdb=" O3'   C A 624 "
        pdb=" P     G A 625 "
        pdb=" OP2   G A 625 "
      ideal   model   delta    sigma   weight residual
     108.00   84.09   23.91 3.00e+00 1.11e-01 6.35e+01
  angle pdb=" O3'   C A 624 "
        pdb=" P     G A 625 "
        pdb=" O5'   G A 625 "
      ideal   model   delta    sigma   weight residual
     104.00   98.81    5.19 1.50e+00 4.44e-01 1.20e+01
  angle pdb=" OP1   G A 625 "
        pdb=" P     G A 625 "
        pdb=" OP2   G A 625 "
      ideal   model   delta    sigma   weight residual
     119.60  129.76  -10.16 3.00e+00 1.11e-01 1.15e+01
  angle pdb=" C6    A A 278 "
        pdb=" N1    A A 278 "
        pdb=" C2    A A 278 "
      ideal   model   delta    sigma   weight residual
     118.60  127.77   -9.17 3.00e+00 1.11e-01 9.34e+00
  ... (remaining 29889 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.82: 11083
       35.82 -    71.63: 1350
       71.63 -   107.45: 182
      107.45 -   143.27: 2
      143.27 -   179.09: 3
  Dihedral angle restraints: 12620
    sinusoidal: 11102
      harmonic: 1518
  Sorted by residual:
  dihedral pdb=" O4'   C A 140 "
           pdb=" C1'   C A 140 "
           pdb=" N1    C A 140 "
           pdb=" C2    C A 140 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   35.65 -163.65     1      1.70e+01 3.46e-03 6.51e+01
  dihedral pdb=" O4'   U A1313 "
           pdb=" C1'   U A1313 "
           pdb=" N1    U A1313 "
           pdb=" C2    U A1313 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00  108.07   91.93     1      1.50e+01 4.44e-03 4.41e+01
  dihedral pdb=" O4'   A A 632 "
           pdb=" C1'   A A 632 "
           pdb=" N9    A A 632 "
           pdb=" C4    A A 632 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.00  128.32  -60.32     1      1.70e+01 3.46e-03 1.68e+01
  ... (remaining 12617 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.400: 3912
       0.400 -    0.801: 0
       0.801 -    1.201: 0
       1.201 -    1.602: 0
       1.602 -    2.002: 1
  Chirality restraints: 3913
  Sorted by residual:
  chirality pdb=" P     G A 625 "
            pdb=" OP1   G A 625 "
            pdb=" OP2   G A 625 "
            pdb=" O5'   G A 625 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    0.41    2.00 2.00e-01 2.50e+01 1.00e+02
  chirality pdb=" CA  ILE E 148 "
            pdb=" N   ILE E 148 "
            pdb=" C   ILE E 148 "
            pdb=" CB  ILE E 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.63e-01
  chirality pdb=" C3'   U A 148 "
            pdb=" C4'   U A 148 "
            pdb=" O3'   U A 148 "
            pdb=" C2'   U A 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.60   -0.15 2.00e-01 2.50e+01 5.50e-01
  ... (remaining 3910 not shown)

  Planarity restraints: 1349
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A  33 "    0.009 2.00e-02 2.50e+03   1.24e-02 3.47e+00
        pdb=" N1    C A  33 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    C A  33 "    0.025 2.00e-02 2.50e+03
        pdb=" O2    C A  33 "   -0.022 2.00e-02 2.50e+03
        pdb=" N3    C A  33 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    C A  33 "    0.005 2.00e-02 2.50e+03
        pdb=" N4    C A  33 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    C A  33 "   -0.009 2.00e-02 2.50e+03
        pdb=" C6    C A  33 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 363 "   -0.007 2.00e-02 2.50e+03   1.00e-02 3.01e+00
        pdb=" N9    G A 363 "    0.004 2.00e-02 2.50e+03
        pdb=" C8    G A 363 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    G A 363 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    G A 363 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G A 363 "    0.002 2.00e-02 2.50e+03
        pdb=" O6    G A 363 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    G A 363 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    G A 363 "    0.027 2.00e-02 2.50e+03
        pdb=" N2    G A 363 "   -0.019 2.00e-02 2.50e+03
        pdb=" N3    G A 363 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    G A 363 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G A 473 "    0.006 2.00e-02 2.50e+03   9.37e-03 2.63e+00
        pdb=" N9    G A 473 "   -0.002 2.00e-02 2.50e+03
        pdb=" C8    G A 473 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7    G A 473 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G A 473 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    G A 473 "   -0.005 2.00e-02 2.50e+03
        pdb=" O6    G A 473 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    G A 473 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G A 473 "   -0.025 2.00e-02 2.50e+03
        pdb=" N2    G A 473 "    0.017 2.00e-02 2.50e+03
        pdb=" N3    G A 473 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G A 473 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1346 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 160
        2.52 -     3.11: 13075
        3.11 -     3.71: 33605
        3.71 -     4.30: 45916
        4.30 -     4.90: 62873
  Nonbonded interactions: 155629
  Sorted by model distance:
  nonbonded pdb=" O2'   A A 255 "
            pdb=" O4'   A A 256 "
     model   vdw
     1.924 3.040
  nonbonded pdb=" O2    C A  69 "
            pdb=" O2'   A A  73 "
     model   vdw
     1.948 3.040
  nonbonded pdb=" O2    C A 106 "
            pdb=" O2'   A A 294 "
     model   vdw
     1.965 3.040
  nonbonded pdb=" O2'   A A 126 "
            pdb=" O4'   A A 127 "
     model   vdw
     1.975 3.040
  nonbonded pdb=" O2'   A A 299 "
            pdb=" O4'   A A 300 "
     model   vdw
     1.988 3.040
  ... (remaining 155624 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     20.210
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
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      :  0.001   0.033  19762  Z= 0.073
  Angle     :  0.451  26.711  29894  Z= 0.212
  Chirality :  0.040   2.002   3913
  Planarity :  0.002   0.022   1349
  Dihedral  : 22.913 179.086  11622
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.39 %
    Favored  : 96.39 %
  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:  1.73 (0.39), residues: 507
  helix:  2.53 (0.37), residues: 213
  sheet:  0.56 (0.67), residues: 71
  loop :  0.03 (0.42), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG 2  35 
 TYR   0.005   0.001   TYR T  84 
 PHE   0.005   0.001   PHE S  75 
 TRP   0.003   0.001   TRP T  80 
 HIS   0.001   0.000   HIS S 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00135 (19762)
  covalent geometry    : angle       0.45142 (29894)
  hydrogen bonds       : bond        0.07736 (  687)
  hydrogen bonds       : angle       4.05371 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8920 (tm-30)
REVERT: E  149 ILE cc_start: 0.9481 (tp) cc_final: 0.8987 (tp)
REVERT: E  188 MET cc_start: 0.8631 (ttt) cc_final: 0.8222 (tpt)
REVERT: E  195 GLN cc_start: 0.9690 (mt0) cc_final: 0.9289 (mt0)
REVERT: E  199 MET cc_start: 0.8842 (mtm) cc_final: 0.8132 (ptp)
REVERT: S   68 ASP cc_start: 0.9274 (t0) cc_final: 0.8858 (t70)
REVERT: U   12 VAL cc_start: 0.8571 (t) cc_final: 0.8029 (t)
REVERT: T    1 MET cc_start: 0.6162 (pmm) cc_final: 0.5517 (pmm)
REVERT: T   80 TRP cc_start: 0.6633 (p-90) cc_final: 0.6382 (t60)
  outliers start: 1
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1740
  time to fit residues: 25.5941
Evaluate side-chains
  63 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:   20.0000
   chunk 100 optimal weight:    4.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
2  13 ASN
E  30 GLN
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 136 GLN
** U  45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  48 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.057041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.043191 restraints weight = 206189.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.044322 restraints weight = 83273.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.044951 restraints weight = 51737.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.045253 restraints weight = 41494.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.045335 restraints weight = 37816.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  19762  Z= 0.188
  Angle     :  0.644  27.737  29894  Z= 0.308
  Chirality :  0.043   1.956   3913
  Planarity :  0.004   0.052   1349
  Dihedral  : 23.894 169.642  10573
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.61 %
    Favored  : 96.16 %
  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:  0.48 (0.37), residues: 507
  helix:  1.21 (0.34), residues: 219
  sheet: -0.27 (0.57), residues: 93
  loop : -0.28 (0.43), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG Y  29 
 TYR   0.009   0.002   TYR T  84 
 PHE   0.017   0.002   PHE Y  26 
 TRP   0.012   0.005   TRP T  80 
 HIS   0.003   0.001   HIS 2  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (19762)
  covalent geometry    : angle       0.64364 (29894)
  hydrogen bonds       : bond        0.07791 (  687)
  hydrogen bonds       : angle       3.79613 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   97 ASN cc_start: 0.8689 (t0) cc_final: 0.7866 (t0)
REVERT: E  163 ASN cc_start: 0.8476 (t0) cc_final: 0.7985 (m-40)
REVERT: E  199 MET cc_start: 0.9003 (mtm) cc_final: 0.8398 (ptp)
REVERT: S   68 ASP cc_start: 0.9463 (t0) cc_final: 0.9230 (t70)
REVERT: U   12 VAL cc_start: 0.8871 (t) cc_final: 0.7957 (t)
REVERT: T   11 LEU cc_start: 0.8715 (pt) cc_final: 0.8416 (pp)
REVERT: T   51 PHE cc_start: 0.8753 (m-80) cc_final: 0.8451 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 86
  average time/residue: 0.1678
  time to fit residues: 20.9198
Evaluate side-chains
  69 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 68
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 89 optimal weight:   20.0000
   chunk 72 optimal weight:    3.9990
   chunk 85 optimal weight:    0.3980
   chunk 25 optimal weight:   10.0000
   chunk 59 optimal weight:   30.0000
   chunk 45 optimal weight:   10.0000
   chunk 8 optimal weight:   10.0000
   chunk 60 optimal weight:   20.0000
   chunk 58 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    6.2788

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

Flipped N/Q/H residues before XYZ refinement:
2  13 ASN
** E  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  30 GLN
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T  48 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.049466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.035547 restraints weight = 209422.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.036043 restraints weight = 120254.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.036112 restraints weight = 73173.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.036697 restraints weight = 70444.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.036620 restraints weight = 60914.386|
|-----------------------------------------------------------------------------|
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.6106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047  19762  Z= 0.351
  Angle     :  0.892  27.570  29894  Z= 0.431
  Chirality :  0.052   1.951   3913
  Planarity :  0.007   0.082   1349
  Dihedral  : 25.243 172.432  10573
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 34.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  4.97 %
    Favored  : 94.36 %
  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: -0.67 (0.35), residues: 507
  helix:  0.09 (0.32), residues: 215
  sheet: -0.94 (0.56), residues: 86
  loop : -0.61 (0.43), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG Y  52 
 TYR   0.023   0.003   TYR T  84 
 PHE   0.025   0.003   PHE Y  26 
 TRP   0.019   0.006   TRP T  80 
 HIS   0.010   0.002   HIS Y  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00651 (19762)
  covalent geometry    : angle       0.89220 (29894)
  hydrogen bonds       : bond        0.11809 (  687)
  hydrogen bonds       : angle       4.58641 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  102 ARG cc_start: 0.9431 (ptt180) cc_final: 0.9163 (ptt90)
REVERT: E  199 MET cc_start: 0.9221 (mtm) cc_final: 0.8605 (mtp)
REVERT: Y   30 MET cc_start: 0.8500 (mmm) cc_final: 0.8169 (mmm)
REVERT: T   31 VAL cc_start: 0.8740 (m) cc_final: 0.8443 (t)
REVERT: T   32 LEU cc_start: 0.8923 (mt) cc_final: 0.8558 (mp)
REVERT: T   87 LEU cc_start: 0.8285 (mt) cc_final: 0.7982 (mp)
  outliers start: 3
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1646
  time to fit residues: 19.0157
Evaluate side-chains
  50 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 87 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   chunk 72 optimal weight:    0.0070
   chunk 6 optimal weight:    6.9990
   chunk 41 optimal weight:    8.9990
   chunk 99 optimal weight:    5.9990
   chunk 101 optimal weight:    0.2980
   chunk 40 optimal weight:    9.9990
   chunk 69 optimal weight:    0.0870
   chunk 52 optimal weight:   10.0000
   overall best weight:    2.0780

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

Flipped N/Q/H residues before XYZ refinement:
E  24 ASN
S  15 GLN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  68 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.051990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.037498 restraints weight = 200322.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.038632 restraints weight = 76607.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.039264 restraints weight = 47804.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.039559 restraints weight = 38455.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.039650 restraints weight = 35096.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.5537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  19762  Z= 0.146
  Angle     :  0.611  27.122  29894  Z= 0.293
  Chirality :  0.043   1.955   3913
  Planarity :  0.004   0.050   1349
  Dihedral  : 24.693 164.358  10573
  Min Nonbonded Distance : 2.052

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  5.19 %
    Favored  : 94.58 %
  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: -0.36 (0.35), residues: 507
  helix:  0.46 (0.32), residues: 219
  sheet: -0.63 (0.53), residues: 89
  loop : -0.68 (0.43), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG Y  29 
 TYR   0.011   0.002   TYR T  84 
 PHE   0.015   0.001   PHE Y  26 
 TRP   0.035   0.008   TRP T  80 
 HIS   0.003   0.001   HIS Y  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (19762)
  covalent geometry    : angle       0.61085 (29894)
  hydrogen bonds       : bond        0.06431 (  687)
  hydrogen bonds       : angle       3.85834 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 84
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  100 MET cc_start: 0.9436 (mtt) cc_final: 0.9054 (mtp)
REVERT: E  102 ARG cc_start: 0.9330 (ptt180) cc_final: 0.8959 (ptt-90)
REVERT: E  195 GLN cc_start: 0.9698 (mt0) cc_final: 0.9264 (mt0)
REVERT: E  199 MET cc_start: 0.9230 (mtm) cc_final: 0.8564 (mtp)
REVERT: S   11 ARG cc_start: 0.8193 (mpp-170) cc_final: 0.7850 (mpp80)
REVERT: S   68 ASP cc_start: 0.9513 (t0) cc_final: 0.9249 (t70)
REVERT: U    7 ASP cc_start: 0.8943 (m-30) cc_final: 0.8667 (m-30)
REVERT: T   31 VAL cc_start: 0.8868 (m) cc_final: 0.8521 (t)
REVERT: T   32 LEU cc_start: 0.8692 (mt) cc_final: 0.8330 (mp)
REVERT: T   51 PHE cc_start: 0.8816 (m-80) cc_final: 0.8480 (m-80)
REVERT: T   80 TRP cc_start: 0.7087 (t60) cc_final: 0.6875 (t60)
REVERT: T   87 LEU cc_start: 0.8565 (mt) cc_final: 0.8331 (mp)
  outliers start: 1
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1699
  time to fit residues: 20.7916
Evaluate side-chains
  64 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 97 optimal weight:    4.9990
   chunk 96 optimal weight:    8.9990
   chunk 60 optimal weight:   20.0000
   chunk 80 optimal weight:    0.5980
   chunk 69 optimal weight:   10.0000
   chunk 52 optimal weight:   10.0000
   chunk 108 optimal weight:   50.0000
   chunk 43 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   overall best weight:    6.9190

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

Flipped N/Q/H residues before XYZ refinement:
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  52 ASN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  68 ASN
Y  15 ASN
Y  20 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T  15 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.048200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.033631 restraints weight = 212621.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.034594 restraints weight = 89363.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.035095 restraints weight = 58782.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.035277 restraints weight = 49455.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.035334 restraints weight = 46396.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.7332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047  19762  Z= 0.376
  Angle     :  0.896  27.558  29894  Z= 0.430
  Chirality :  0.053   1.921   3913
  Planarity :  0.007   0.105   1349
  Dihedral  : 25.562 176.995  10573
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 35.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.84 %
    Favored  : 95.94 %
  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: -1.26 (0.34), residues: 507
  helix: -0.28 (0.31), residues: 219
  sheet: -1.49 (0.54), residues: 91
  loop : -0.93 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG U  81 
 TYR   0.016   0.002   TYR T  84 
 PHE   0.020   0.003   PHE Y  26 
 TRP   0.003   0.002   TRP T  80 
 HIS   0.006   0.002   HIS E 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00696 (19762)
  covalent geometry    : angle       0.89595 (29894)
  hydrogen bonds       : bond        0.11862 (  687)
  hydrogen bonds       : angle       4.52473 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  102 ARG cc_start: 0.9384 (ptt180) cc_final: 0.9155 (ptt90)
REVERT: E  199 MET cc_start: 0.9286 (mtm) cc_final: 0.8744 (mtm)
REVERT: S   68 ASP cc_start: 0.9499 (t0) cc_final: 0.9274 (t0)
REVERT: T   31 VAL cc_start: 0.9194 (m) cc_final: 0.8963 (t)
REVERT: T   32 LEU cc_start: 0.8754 (mt) cc_final: 0.8517 (mt)
REVERT: T   80 TRP cc_start: 0.7126 (t60) cc_final: 0.6824 (t60)
REVERT: T   87 LEU cc_start: 0.8526 (mt) cc_final: 0.8254 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 77
  average time/residue: 0.1423
  time to fit residues: 16.0046
Evaluate side-chains
  54 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 44 optimal weight:   10.0000
   chunk 62 optimal weight:   20.0000
   chunk 27 optimal weight:   10.0000
   chunk 18 optimal weight:   20.0000
   chunk 38 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 33 optimal weight:    7.9990
   chunk 34 optimal weight:   10.0000
   overall best weight:    7.9992

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

Flipped N/Q/H residues before XYZ refinement:
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  60 HIS
S  61 ASN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T  15 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.047802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.033833 restraints weight = 221221.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.034789 restraints weight = 92102.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.035320 restraints weight = 59376.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.035533 restraints weight = 49094.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.035679 restraints weight = 45398.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.9072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.046  19762  Z= 0.410
  Angle     :  0.969  27.279  29894  Z= 0.471
  Chirality :  0.056   1.918   3913
  Planarity :  0.007   0.081   1349
  Dihedral  : 26.263 172.900  10573
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 42.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  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: -1.93 (0.34), residues: 507
  helix: -0.73 (0.32), residues: 218
  sheet: -2.05 (0.51), residues: 90
  loop : -1.32 (0.41), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG U  81 
 TYR   0.020   0.003   TYR T  84 
 PHE   0.027   0.003   PHE 2  18 
 TRP   0.004   0.002   TRP T  80 
 HIS   0.006   0.002   HIS E 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00758 (19762)
  covalent geometry    : angle       0.96897 (29894)
  hydrogen bonds       : bond        0.12958 (  687)
  hydrogen bonds       : angle       4.90381 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   22 MET cc_start: 0.8504 (ttt) cc_final: 0.8228 (ttt)
REVERT: E  102 ARG cc_start: 0.9278 (ptt180) cc_final: 0.9059 (ptt90)
REVERT: E  114 ARG cc_start: 0.8879 (ptp90) cc_final: 0.8634 (ptt180)
REVERT: E  199 MET cc_start: 0.9350 (mtm) cc_final: 0.8528 (mtm)
REVERT: T   31 VAL cc_start: 0.9237 (m) cc_final: 0.8793 (t)
REVERT: T   32 LEU cc_start: 0.8671 (mt) cc_final: 0.8386 (mp)
REVERT: T   79 ASP cc_start: 0.8474 (m-30) cc_final: 0.8144 (m-30)
REVERT: T   80 TRP cc_start: 0.6632 (t60) cc_final: 0.6319 (t60)
REVERT: T   87 LEU cc_start: 0.8651 (mt) cc_final: 0.8363 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1782
  time to fit residues: 19.3037
Evaluate side-chains
  52 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 113 optimal weight:    8.9990
   chunk 53 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   chunk 42 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    7.7992

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

Flipped N/Q/H residues before XYZ refinement:
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  31 GLN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.046337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.031823 restraints weight = 216205.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.032764 restraints weight = 93652.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.033284 restraints weight = 61108.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.033532 restraints weight = 50439.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.033566 restraints weight = 46473.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.9541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.063  19762  Z= 0.407
  Angle     :  0.947  27.549  29894  Z= 0.459
  Chirality :  0.055   1.904   3913
  Planarity :  0.007   0.055   1349
  Dihedral  : 26.354 171.972  10573
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 43.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.84 %
    Favored  : 95.94 %
  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: -2.42 (0.34), residues: 507
  helix: -1.09 (0.31), residues: 223
  sheet: -2.04 (0.52), residues: 85
  loop : -1.79 (0.41), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG U  81 
 TYR   0.016   0.002   TYR T  84 
 PHE   0.024   0.003   PHE 2  18 
 TRP   0.004   0.001   TRP T  80 
 HIS   0.004   0.002   HIS 2  16 

Details of bonding type rmsd
  covalent geometry    : bond        0.00756 (19762)
  covalent geometry    : angle       0.94661 (29894)
  hydrogen bonds       : bond        0.12801 (  687)
  hydrogen bonds       : angle       4.81168 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 70
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   22 MET cc_start: 0.8674 (ttt) cc_final: 0.8408 (ttt)
REVERT: E  102 ARG cc_start: 0.9228 (ptt180) cc_final: 0.9004 (ptt90)
REVERT: E  199 MET cc_start: 0.9438 (mtm) cc_final: 0.8981 (mtm)
REVERT: Y    4 LYS cc_start: 0.9583 (pptt) cc_final: 0.9344 (pptt)
REVERT: T   31 VAL cc_start: 0.9137 (m) cc_final: 0.8668 (t)
REVERT: T   32 LEU cc_start: 0.8593 (mt) cc_final: 0.8310 (mp)
REVERT: T   51 PHE cc_start: 0.8695 (m-80) cc_final: 0.8427 (m-80)
REVERT: T   79 ASP cc_start: 0.8409 (m-30) cc_final: 0.8107 (m-30)
REVERT: T   80 TRP cc_start: 0.6546 (t60) cc_final: 0.6102 (t60)
REVERT: T   87 LEU cc_start: 0.8733 (mt) cc_final: 0.8485 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 71
  average time/residue: 0.1681
  time to fit residues: 17.2815
Evaluate side-chains
  54 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 56 optimal weight:   20.0000
   chunk 5 optimal weight:    7.9990
   chunk 57 optimal weight:   20.0000
   chunk 4 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 36 optimal weight:   20.0000
   chunk 18 optimal weight:   20.0000
   chunk 114 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    7.3990

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

Flipped N/Q/H residues before XYZ refinement:
2  16 HIS
S  15 GLN
U  52 ASN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  68 ASN
Y  15 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.046161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.031911 restraints weight = 214681.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.032851 restraints weight = 90651.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.033379 restraints weight = 58824.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.033549 restraints weight = 48489.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.033714 restraints weight = 45193.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          1.0024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059  19762  Z= 0.389
  Angle     :  0.932  27.336  29894  Z= 0.452
  Chirality :  0.055   1.910   3913
  Planarity :  0.006   0.052   1349
  Dihedral  : 26.501 175.349  10573
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 42.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.48 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  :  2.26 %
    Favored  : 97.29 %
  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: -2.67 (0.33), residues: 507
  helix: -1.18 (0.30), residues: 222
  sheet: -2.25 (0.51), residues: 81
  loop : -2.07 (0.39), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG U  81 
 TYR   0.012   0.003   TYR T  84 
 PHE   0.018   0.003   PHE Y  26 
 TRP   0.003   0.001   TRP T  80 
 HIS   0.006   0.002   HIS E 165 

Details of bonding type rmsd
  covalent geometry    : bond        0.00720 (19762)
  covalent geometry    : angle       0.93236 (29894)
  hydrogen bonds       : bond        0.12626 (  687)
  hydrogen bonds       : angle       4.81510 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   22 MET cc_start: 0.8690 (ttt) cc_final: 0.8207 (ttt)
REVERT: E  102 ARG cc_start: 0.9268 (ptt180) cc_final: 0.9060 (ptt90)
REVERT: E  184 ASP cc_start: 0.9286 (t70) cc_final: 0.8837 (t0)
REVERT: E  199 MET cc_start: 0.9442 (mtm) cc_final: 0.8721 (mtm)
REVERT: Y    7 ARG cc_start: 0.9283 (ptp-110) cc_final: 0.8710 (ttp80)
REVERT: T   31 VAL cc_start: 0.9024 (m) cc_final: 0.8583 (t)
REVERT: T   32 LEU cc_start: 0.8672 (mt) cc_final: 0.8449 (mt)
REVERT: T   51 PHE cc_start: 0.8792 (m-80) cc_final: 0.8452 (m-80)
REVERT: T   79 ASP cc_start: 0.8382 (m-30) cc_final: 0.8031 (m-30)
REVERT: T   80 TRP cc_start: 0.6419 (t60) cc_final: 0.5922 (t60)
REVERT: T   87 LEU cc_start: 0.9032 (mt) cc_final: 0.8732 (mt)
  outliers start: 2
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1429
  time to fit residues: 15.7092
Evaluate side-chains
  54 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 56 optimal weight:   20.0000
   chunk 38 optimal weight:    9.9990
   chunk 100 optimal weight:    4.9990
   chunk 102 optimal weight:    6.9990
   chunk 75 optimal weight:    7.9990
   chunk 43 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   chunk 36 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.046344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.032148 restraints weight = 211290.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.033037 restraints weight = 89236.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.033566 restraints weight = 58303.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.033778 restraints weight = 48020.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.033854 restraints weight = 44367.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          1.0093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  19762  Z= 0.341
  Angle     :  0.864  27.296  29894  Z= 0.419
  Chirality :  0.052   1.918   3913
  Planarity :  0.006   0.054   1349
  Dihedral  : 26.395 178.505  10573
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 37.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  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: -2.54 (0.34), residues: 507
  helix: -0.93 (0.32), residues: 223
  sheet: -2.36 (0.48), residues: 82
  loop : -2.10 (0.40), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG U  81 
 TYR   0.012   0.003   TYR T  84 
 PHE   0.020   0.003   PHE Y  26 
 TRP   0.004   0.001   TRP T  80 
 HIS   0.005   0.001   HIS S  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00632 (19762)
  covalent geometry    : angle       0.86445 (29894)
  hydrogen bonds       : bond        0.11410 (  687)
  hydrogen bonds       : angle       4.71178 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   22 MET cc_start: 0.8764 (ttt) cc_final: 0.8509 (ttt)
REVERT: E   30 GLN cc_start: 0.9684 (pt0) cc_final: 0.9465 (pt0)
REVERT: E  102 ARG cc_start: 0.9278 (ptt180) cc_final: 0.9069 (ptt90)
REVERT: E  199 MET cc_start: 0.9362 (mtm) cc_final: 0.8480 (mtm)
REVERT: Y    7 ARG cc_start: 0.9265 (ptp-110) cc_final: 0.8778 (ttp80)
REVERT: T   31 VAL cc_start: 0.9145 (m) cc_final: 0.8755 (t)
REVERT: T   32 LEU cc_start: 0.8558 (mt) cc_final: 0.8324 (mt)
REVERT: T   51 PHE cc_start: 0.8759 (m-80) cc_final: 0.8360 (m-80)
REVERT: T   79 ASP cc_start: 0.8445 (m-30) cc_final: 0.8087 (m-30)
REVERT: T   80 TRP cc_start: 0.6570 (t60) cc_final: 0.5984 (t60)
REVERT: T   87 LEU cc_start: 0.9137 (mt) cc_final: 0.8790 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1591
  time to fit residues: 16.8240
Evaluate side-chains
  55 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 114 optimal weight:   20.0000
   chunk 64 optimal weight:   30.0000
   chunk 6 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 0 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 96 optimal weight:    0.4980
   chunk 90 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    3.0988

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

Flipped N/Q/H residues before XYZ refinement:
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  52 ASN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.049084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.035509 restraints weight = 210340.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.036486 restraints weight = 81486.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.037053 restraints weight = 50240.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.037350 restraints weight = 40942.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.037428 restraints weight = 37329.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.9549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  19762  Z= 0.188
  Angle     :  0.700  27.126  29894  Z= 0.338
  Chirality :  0.047   1.942   3913
  Planarity :  0.005   0.037   1349
  Dihedral  : 25.835 172.391  10573
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 23.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.68 %
    Favored  : 99.10 %
  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: -1.94 (0.34), residues: 507
  helix: -0.42 (0.33), residues: 223
  sheet: -1.71 (0.52), residues: 70
  loop : -2.01 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG T   3 
 TYR   0.009   0.002   TYR T  84 
 PHE   0.015   0.002   PHE Y  26 
 TRP   0.003   0.001   TRP T  80 
 HIS   0.003   0.001   HIS S  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (19762)
  covalent geometry    : angle       0.69968 (29894)
  hydrogen bonds       : bond        0.08282 (  687)
  hydrogen bonds       : angle       4.19046 ( 1350)

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  102 ARG cc_start: 0.9213 (ptt180) cc_final: 0.8840 (mtm-85)
REVERT: E  199 MET cc_start: 0.9312 (mtm) cc_final: 0.8460 (mtm)
REVERT: Y    4 LYS cc_start: 0.9454 (pptt) cc_final: 0.9188 (pptt)
REVERT: Y    7 ARG cc_start: 0.9333 (ptp-110) cc_final: 0.8653 (ttp80)
REVERT: T   29 THR cc_start: 0.7729 (m) cc_final: 0.7458 (m)
REVERT: T   31 VAL cc_start: 0.9043 (m) cc_final: 0.8704 (t)
REVERT: T   32 LEU cc_start: 0.8635 (mt) cc_final: 0.8397 (mt)
REVERT: T   51 PHE cc_start: 0.8810 (m-80) cc_final: 0.8402 (m-80)
REVERT: T   79 ASP cc_start: 0.8544 (m-30) cc_final: 0.8203 (m-30)
REVERT: T   80 TRP cc_start: 0.6524 (t60) cc_final: 0.5981 (t60)
REVERT: T   87 LEU cc_start: 0.9092 (mt) cc_final: 0.8869 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1492
  time to fit residues: 16.9909
Evaluate side-chains
  53 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 105 optimal weight:    4.9990
   chunk 80 optimal weight:    8.9990
   chunk 64 optimal weight:   30.0000
   chunk 18 optimal weight:   20.0000
   chunk 21 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 38 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y  15 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** T  15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.046468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.032187 restraints weight = 209623.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.033188 restraints weight = 83913.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.033732 restraints weight = 53048.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.033925 restraints weight = 43380.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.034069 restraints weight = 40206.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          1.0109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  19762  Z= 0.326
  Angle     :  0.836  27.335  29894  Z= 0.405
  Chirality :  0.051   1.916   3913
  Planarity :  0.006   0.051   1349
  Dihedral  : 26.223 179.550  10573
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 34.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.66 %
    Favored  : 90.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  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: -2.19 (0.34), residues: 507
  helix: -0.73 (0.32), residues: 223
  sheet: -1.62 (0.53), residues: 70
  loop : -2.10 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG Y  47 
 TYR   0.011   0.002   TYR T  84 
 PHE   0.014   0.002   PHE Y  26 
 TRP   0.004   0.001   TRP T  80 
 HIS   0.003   0.001   HIS S  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00604 (19762)
  covalent geometry    : angle       0.83596 (29894)
  hydrogen bonds       : bond        0.10941 (  687)
  hydrogen bonds       : angle       4.52063 ( 1350)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2561.23 seconds
wall clock time: 45 minutes 41.57 seconds (2741.57 seconds total)