Starting phenix.real_space_refine
on Sun Jun 15 23:24:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c9a_16507/06_2025/8c9a_16507.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c9a_16507/06_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_16507/06_2025/8c9a_16507.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c9a_16507/06_2025/8c9a_16507.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c9a_16507/06_2025/8c9a_16507.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c9a_16507/06_2025/8c9a_16507.cif"
  }
  resolution = 4.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.044
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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.31, per 1000 atoms: 0.57
  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: 4.21
  Conformation dependent library (CDL) restraints added in 749.2 milliseconds
  

  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: 8.01
  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: 8.70

  Time building geometry restraints manager: 5.10 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:             2.230
  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:             0.020
  Extract box with map and model:          0.680
  Check model and map are aligned:         0.120
  Set scattering table:                    0.170
  Process input model:                     46.090
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   52.340
-------------------------------------------------------------------------------
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 : 6.58
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (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
 TRP   0.003   0.001   TRP T  80 
 HIS   0.001   0.000   HIS S 102 
 PHE   0.005   0.001   PHE S  75 
 TYR   0.005   0.001   TYR T  84 
 ARG   0.002   0.000   ARG 2  35 

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

*********************** 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  : 0.856 
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: 0.3407
  time to fit residues: 50.0090
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  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   chunk 58 optimal weight:   20.0000
   chunk 46 optimal weight:    7.9990
   chunk 90 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 67 optimal weight:    4.9990
   chunk 104 optimal weight:    0.0030
   overall best weight:    4.7998

-------------------------------------------------------------------------------
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**
E 136 GLN
** 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**
T  15 HIS
T  48 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.052942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.038414 restraints weight = 203665.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.039481 restraints weight = 83620.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.040075 restraints weight = 53698.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.3929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  19762  Z= 0.289
  Angle     :  0.796  27.964  29894  Z= 0.381
  Chirality :  0.048   1.932   3913
  Planarity :  0.006   0.075   1349
  Dihedral  : 24.376 173.308  10573
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 22.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  4.74 %
    Favored  : 95.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.36), residues: 507
  helix:  0.79 (0.33), residues: 220
  sheet:  0.29 (0.58), residues: 79
  loop : -0.54 (0.42), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP T  80 
 HIS   0.006   0.001   HIS S  60 
 PHE   0.021   0.002   PHE Y  26 
 TYR   0.012   0.002   TYR T  84 
 ARG   0.007   0.001   ARG U  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10056 (  687)
  hydrogen bonds       : angle       4.14621 ( 1350)
  covalent geometry    : bond        0.00535 (19762)
  covalent geometry    : angle       0.79601 (29894)

*********************** 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
  83 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   97 ASN cc_start: 0.8769 (t0) cc_final: 0.8083 (t0)
REVERT: E  163 ASN cc_start: 0.8537 (t0) cc_final: 0.8040 (m-40)
REVERT: E  188 MET cc_start: 0.9046 (ttt) cc_final: 0.8555 (tpt)
REVERT: E  199 MET cc_start: 0.9087 (mtm) cc_final: 0.8462 (ptp)
REVERT: S   68 ASP cc_start: 0.9516 (t0) cc_final: 0.9294 (t70)
REVERT: U   17 ASP cc_start: 0.7924 (t0) cc_final: 0.7638 (t0)
REVERT: T   11 LEU cc_start: 0.8711 (pt) cc_final: 0.8452 (pp)
REVERT: T   51 PHE cc_start: 0.8810 (m-80) cc_final: 0.8536 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 82
  average time/residue: 0.3114
  time to fit residues: 38.1759
Evaluate side-chains
  59 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 99 optimal weight:    6.9990
   chunk 68 optimal weight:    9.9990
   chunk 81 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 88 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 113 optimal weight:    0.0670
   chunk 114 optimal weight:    7.9990
   chunk 87 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    4.6126

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

Flipped N/Q/H residues before XYZ refinement:
E  30 GLN
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T  15 HIS
T  48 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.050787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.036952 restraints weight = 201549.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.037459 restraints weight = 113535.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.037572 restraints weight = 69390.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.5685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  19762  Z= 0.251
  Angle     :  0.733  26.753  29894  Z= 0.353
  Chirality :  0.047   1.952   3913
  Planarity :  0.006   0.088   1349
  Dihedral  : 24.992 168.520  10573
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 24.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  2.71 %
    Favored  : 97.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.36), residues: 507
  helix:  0.54 (0.33), residues: 218
  sheet: -0.94 (0.52), residues: 96
  loop : -0.61 (0.43), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP T  80 
 HIS   0.006   0.002   HIS Y  41 
 PHE   0.022   0.002   PHE Y  26 
 TYR   0.016   0.002   TYR T  84 
 ARG   0.007   0.001   ARG E 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08321 (  687)
  hydrogen bonds       : angle       4.23938 ( 1350)
  covalent geometry    : bond        0.00466 (19762)
  covalent geometry    : angle       0.73287 (29894)

*********************** 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
  83 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 GLU cc_start: 0.9277 (tm-30) cc_final: 0.9018 (tm-30)
REVERT: E  100 MET cc_start: 0.9494 (mtt) cc_final: 0.9049 (mtp)
REVERT: E  102 ARG cc_start: 0.9269 (ptt-90) cc_final: 0.9038 (ptp90)
REVERT: E  149 ILE cc_start: 0.9546 (tp) cc_final: 0.8463 (tp)
REVERT: E  199 MET cc_start: 0.9206 (mtm) cc_final: 0.8347 (ptp)
REVERT: U    7 ASP cc_start: 0.9101 (m-30) cc_final: 0.8867 (m-30)
REVERT: U   52 ASN cc_start: 0.9272 (t0) cc_final: 0.9023 (p0)
REVERT: T   31 VAL cc_start: 0.8796 (m) cc_final: 0.8522 (t)
REVERT: T   32 LEU cc_start: 0.8888 (mt) cc_final: 0.8533 (mp)
REVERT: T   51 PHE cc_start: 0.8920 (m-80) cc_final: 0.8552 (m-80)
REVERT: T   87 LEU cc_start: 0.8299 (mt) cc_final: 0.8006 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 83
  average time/residue: 0.3300
  time to fit residues: 40.5698
Evaluate side-chains
  59 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 73 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0770
   chunk 65 optimal weight:   10.0000
   chunk 107 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 86 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9980
   chunk 87 optimal weight:    8.9990
   overall best weight:    4.1942

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

Flipped N/Q/H residues before XYZ refinement:
E  30 GLN
** 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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.049952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.036149 restraints weight = 202760.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.036719 restraints weight = 116977.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.036752 restraints weight = 70055.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.6485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  19762  Z= 0.239
  Angle     :  0.713  27.334  29894  Z= 0.342
  Chirality :  0.046   1.934   3913
  Planarity :  0.005   0.091   1349
  Dihedral  : 25.044 169.812  10573
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 25.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.35), residues: 507
  helix:  0.47 (0.33), residues: 219
  sheet: -1.02 (0.50), residues: 94
  loop : -0.82 (0.42), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP T  80 
 HIS   0.004   0.001   HIS Y  41 
 PHE   0.016   0.002   PHE Y  26 
 TYR   0.011   0.002   TYR T  84 
 ARG   0.007   0.001   ARG U  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08665 (  687)
  hydrogen bonds       : angle       4.17832 ( 1350)
  covalent geometry    : bond        0.00444 (19762)
  covalent geometry    : angle       0.71282 (29894)

*********************** 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
  82 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.884 
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: 2   22 MET cc_start: 0.8366 (ttt) cc_final: 0.8103 (ttt)
REVERT: E   25 GLU cc_start: 0.9213 (tm-30) cc_final: 0.9004 (tm-30)
REVERT: E  199 MET cc_start: 0.9310 (mtm) cc_final: 0.8594 (mtp)
REVERT: S   68 ASP cc_start: 0.9584 (t0) cc_final: 0.9355 (t70)
REVERT: U    7 ASP cc_start: 0.9001 (m-30) cc_final: 0.8775 (m-30)
REVERT: U   52 ASN cc_start: 0.9137 (t0) cc_final: 0.8871 (p0)
REVERT: T   31 VAL cc_start: 0.8779 (m) cc_final: 0.8423 (t)
REVERT: T   32 LEU cc_start: 0.8793 (mt) cc_final: 0.8454 (mp)
REVERT: T   51 PHE cc_start: 0.8723 (m-80) cc_final: 0.8477 (m-80)
REVERT: T   87 LEU cc_start: 0.8363 (mt) cc_final: 0.8123 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.3378
  time to fit residues: 40.5888
Evaluate side-chains
  62 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 107 optimal weight:    2.9990
   chunk 37 optimal weight:   20.0000
   chunk 13 optimal weight:    9.9990
   chunk 109 optimal weight:    0.7980
   chunk 60 optimal weight:   20.0000
   chunk 86 optimal weight:    7.9990
   chunk 82 optimal weight:   10.0000
   chunk 97 optimal weight:    4.9990
   chunk 26 optimal weight:   20.0000
   overall best weight:    5.1588

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

Flipped N/Q/H residues before XYZ refinement:
S  15 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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.048687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.034138 restraints weight = 208958.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.035154 restraints weight = 85956.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.035652 restraints weight = 55721.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.7462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  19762  Z= 0.284
  Angle     :  0.773  27.226  29894  Z= 0.373
  Chirality :  0.049   1.928   3913
  Planarity :  0.006   0.063   1349
  Dihedral  : 25.422 177.226  10573
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 30.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.16 %
    Favored  : 96.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.34), residues: 507
  helix:  0.04 (0.32), residues: 222
  sheet: -0.91 (0.52), residues: 84
  loop : -1.02 (0.41), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP T  80 
 HIS   0.005   0.001   HIS Y  41 
 PHE   0.016   0.003   PHE Y  26 
 TYR   0.016   0.002   TYR T  84 
 ARG   0.010   0.001   ARG U  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09892 (  687)
  hydrogen bonds       : angle       4.37765 ( 1350)
  covalent geometry    : bond        0.00527 (19762)
  covalent geometry    : angle       0.77331 (29894)

*********************** 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
  84 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.909 
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: 0.8478 (ttt) cc_final: 0.8089 (ttt)
REVERT: E   25 GLU cc_start: 0.9301 (tm-30) cc_final: 0.9091 (tm-30)
REVERT: E  199 MET cc_start: 0.9310 (mtm) cc_final: 0.8516 (mtp)
REVERT: U   52 ASN cc_start: 0.8875 (t0) cc_final: 0.8650 (p0)
REVERT: Y    7 ARG cc_start: 0.8911 (mtt90) cc_final: 0.8665 (ttp80)
REVERT: Y   30 MET cc_start: 0.8729 (mmm) cc_final: 0.8386 (tpp)
REVERT: T   31 VAL cc_start: 0.9268 (m) cc_final: 0.9036 (t)
REVERT: T   32 LEU cc_start: 0.8575 (mt) cc_final: 0.8305 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 84
  average time/residue: 0.3500
  time to fit residues: 42.5918
Evaluate side-chains
  57 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 98 optimal weight:    4.9990
   chunk 61 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   chunk 37 optimal weight:   20.0000
   chunk 28 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 69 optimal weight:    9.9990
   chunk 76 optimal weight:    8.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    7.9990

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

Flipped N/Q/H residues before XYZ refinement:
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 136 GLN
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  31 GLN
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**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.047626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.033732 restraints weight = 222346.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.034698 restraints weight = 91313.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.035198 restraints weight = 59417.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.9122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.050  19762  Z= 0.428
  Angle     :  0.997  27.332  29894  Z= 0.482
  Chirality :  0.057   1.908   3913
  Planarity :  0.007   0.064   1349
  Dihedral  : 26.258 173.129  10573
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 45.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.34), residues: 507
  helix: -0.62 (0.32), residues: 221
  sheet: -1.77 (0.55), residues: 79
  loop : -1.71 (0.39), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP T  80 
 HIS   0.007   0.002   HIS E 165 
 PHE   0.034   0.004   PHE 2  18 
 TYR   0.018   0.003   TYR T  84 
 ARG   0.013   0.001   ARG U  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14189 (  687)
  hydrogen bonds       : angle       4.93697 ( 1350)
  covalent geometry    : bond        0.00791 (19762)
  covalent geometry    : angle       0.99747 (29894)

*********************** 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
  70 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.949 
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: 2   22 MET cc_start: 0.8601 (ttt) cc_final: 0.8302 (ttt)
REVERT: E   25 GLU cc_start: 0.9296 (tm-30) cc_final: 0.9083 (tm-30)
REVERT: E  100 MET cc_start: 0.9079 (mtt) cc_final: 0.8643 (mtp)
REVERT: E  199 MET cc_start: 0.9366 (mtm) cc_final: 0.8938 (mtm)
REVERT: Y    4 LYS cc_start: 0.9275 (pttm) cc_final: 0.8855 (pptt)
REVERT: Y   24 GLU cc_start: 0.9374 (mp0) cc_final: 0.9152 (mp0)
  outliers start: 1
  outliers final: 1
  residues processed: 70
  average time/residue: 0.3740
  time to fit residues: 37.9032
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  : 0.897 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   chunk 48 optimal weight:    4.9990
   chunk 99 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 101 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
** E  30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  31 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.050045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.035647 restraints weight = 198513.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.036731 restraints weight = 78385.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.037326 restraints weight = 48763.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.7994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  19762  Z= 0.142
  Angle     :  0.650  27.007  29894  Z= 0.314
  Chirality :  0.045   1.960   3913
  Planarity :  0.004   0.036   1349
  Dihedral  : 25.304 169.296  10573
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 18.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.35), residues: 507
  helix:  0.03 (0.33), residues: 222
  sheet: -1.27 (0.51), residues: 83
  loop : -1.40 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP T  80 
 HIS   0.003   0.001   HIS Y  41 
 PHE   0.017   0.002   PHE U  95 
 TYR   0.010   0.002   TYR T  84 
 ARG   0.005   0.001   ARG 2  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07376 (  687)
  hydrogen bonds       : angle       4.04186 ( 1350)
  covalent geometry    : bond        0.00257 (19762)
  covalent geometry    : angle       0.65034 (29894)

*********************** 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
  74 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.936 
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   29 GLN cc_start: 0.9374 (pt0) cc_final: 0.9107 (pt0)
REVERT: E   25 GLU cc_start: 0.9258 (tm-30) cc_final: 0.9026 (tm-30)
REVERT: E  100 MET cc_start: 0.9300 (mtt) cc_final: 0.8994 (mtp)
REVERT: E  199 MET cc_start: 0.9333 (mtm) cc_final: 0.8696 (ptm)
REVERT: U    7 ASP cc_start: 0.8933 (m-30) cc_final: 0.8715 (m-30)
REVERT: T   31 VAL cc_start: 0.9096 (m) cc_final: 0.8653 (t)
REVERT: T   32 LEU cc_start: 0.8362 (mt) cc_final: 0.8083 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.3540
  time to fit residues: 38.2947
Evaluate side-chains
  58 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 62 optimal weight:   30.0000
   chunk 6 optimal weight:    8.9990
   chunk 75 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 80 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 114 optimal weight:   20.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  52 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.048310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.034373 restraints weight = 216296.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.035376 restraints weight = 84840.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.035957 restraints weight = 53233.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8406
moved from start:          0.8866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  19762  Z= 0.351
  Angle     :  0.844  27.556  29894  Z= 0.408
  Chirality :  0.051   1.892   3913
  Planarity :  0.006   0.046   1349
  Dihedral  : 25.803 179.716  10573
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 35.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.81 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.34), residues: 507
  helix: -0.21 (0.33), residues: 221
  sheet: -1.36 (0.54), residues: 73
  loop : -1.77 (0.38), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP T  80 
 HIS   0.004   0.002   HIS E 165 
 PHE   0.019   0.003   PHE Y  26 
 TYR   0.012   0.002   TYR T  84 
 ARG   0.010   0.001   ARG Y   7 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11075 (  687)
  hydrogen bonds       : angle       4.48493 ( 1350)
  covalent geometry    : bond        0.00649 (19762)
  covalent geometry    : angle       0.84399 (29894)

*********************** 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
  72 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 71
  time to evaluate  : 1.554 
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   25 GLU cc_start: 0.9301 (tm-30) cc_final: 0.9095 (tm-30)
REVERT: E  100 MET cc_start: 0.9269 (mtt) cc_final: 0.8776 (mtp)
REVERT: E  199 MET cc_start: 0.9379 (mtm) cc_final: 0.8961 (mtm)
REVERT: Y    1 MET cc_start: 0.8947 (tpt) cc_final: 0.8740 (tpp)
REVERT: Y    4 LYS cc_start: 0.9374 (pptt) cc_final: 0.9062 (pptt)
REVERT: Y    7 ARG cc_start: 0.9118 (ttp80) cc_final: 0.8883 (ttp80)
REVERT: T   31 VAL cc_start: 0.9220 (m) cc_final: 0.8608 (t)
REVERT: T   32 LEU cc_start: 0.8454 (mt) cc_final: 0.8085 (mp)
REVERT: T   87 LEU cc_start: 0.8763 (mt) cc_final: 0.8514 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 72
  average time/residue: 0.3594
  time to fit residues: 37.2990
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  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 105 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 93 optimal weight:    8.9990
   chunk 71 optimal weight:    2.9990
   chunk 95 optimal weight:   20.0000
   chunk 88 optimal weight:    7.9990
   chunk 15 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   chunk 26 optimal weight:   20.0000
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.049235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.035338 restraints weight = 211545.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.036395 restraints weight = 81039.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.036984 restraints weight = 50635.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.8761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  19762  Z= 0.234
  Angle     :  0.724  27.179  29894  Z= 0.351
  Chirality :  0.047   1.936   3913
  Planarity :  0.005   0.038   1349
  Dihedral  : 25.650 175.459  10573
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 26.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.35), residues: 507
  helix: -0.04 (0.34), residues: 221
  sheet: -1.22 (0.56), residues: 69
  loop : -1.68 (0.39), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP T  80 
 HIS   0.003   0.001   HIS Y  41 
 PHE   0.015   0.002   PHE Y  26 
 TYR   0.011   0.002   TYR T  84 
 ARG   0.007   0.001   ARG Y   7 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08937 (  687)
  hydrogen bonds       : angle       4.26029 ( 1350)
  covalent geometry    : bond        0.00432 (19762)
  covalent geometry    : angle       0.72436 (29894)

*********************** 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
  72 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 GLU cc_start: 0.9280 (tm-30) cc_final: 0.9066 (tm-30)
REVERT: E  199 MET cc_start: 0.9259 (mtm) cc_final: 0.8466 (ptm)
REVERT: U    7 ASP cc_start: 0.9116 (m-30) cc_final: 0.8912 (m-30)
REVERT: T   11 LEU cc_start: 0.8878 (pt) cc_final: 0.8665 (pp)
REVERT: T   31 VAL cc_start: 0.9195 (m) cc_final: 0.8625 (t)
REVERT: T   32 LEU cc_start: 0.8244 (mt) cc_final: 0.7830 (mp)
REVERT: T   87 LEU cc_start: 0.8784 (mt) cc_final: 0.8396 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.3645
  time to fit residues: 38.3981
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  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 48 optimal weight:    7.9990
   chunk 71 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 100 optimal weight:    9.9990
   chunk 18 optimal weight:   20.0000
   chunk 36 optimal weight:   20.0000
   chunk 6 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 98 optimal weight:    6.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    6.5988

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

Flipped N/Q/H residues before XYZ refinement:
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.047696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.034012 restraints weight = 216115.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.034974 restraints weight = 87911.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.035463 restraints weight = 56648.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.9614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  19762  Z= 0.348
  Angle     :  0.870  27.363  29894  Z= 0.423
  Chirality :  0.052   1.914   3913
  Planarity :  0.006   0.076   1349
  Dihedral  : 26.138 176.664  10573
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 37.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.34), residues: 507
  helix: -0.43 (0.33), residues: 223
  sheet: -1.55 (0.53), residues: 73
  loop : -1.89 (0.39), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP T  80 
 HIS   0.005   0.002   HIS S   9 
 PHE   0.018   0.003   PHE Y  26 
 TYR   0.013   0.002   TYR T  84 
 ARG   0.011   0.001   ARG Y   7 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11823 (  687)
  hydrogen bonds       : angle       4.56376 ( 1350)
  covalent geometry    : bond        0.00644 (19762)
  covalent geometry    : angle       0.87041 (29894)

********************** 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
  68 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.848 
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: 2   22 MET cc_start: 0.8500 (ttt) cc_final: 0.8198 (ttt)
REVERT: E   25 GLU cc_start: 0.9312 (tm-30) cc_final: 0.9096 (tm-30)
REVERT: E  100 MET cc_start: 0.9233 (mtt) cc_final: 0.8712 (mtp)
REVERT: E  199 MET cc_start: 0.9411 (mtm) cc_final: 0.8958 (mtm)
REVERT: Y   30 MET cc_start: 0.8877 (mmm) cc_final: 0.8571 (tpp)
REVERT: T   31 VAL cc_start: 0.9161 (m) cc_final: 0.8565 (t)
REVERT: T   32 LEU cc_start: 0.8422 (mt) cc_final: 0.8023 (mp)
REVERT: T   87 LEU cc_start: 0.8969 (mt) cc_final: 0.8581 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.3598
  time to fit residues: 35.3116
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  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 88 optimal weight:    0.6980
   chunk 8 optimal weight:    7.9990
   chunk 14 optimal weight:   20.0000
   chunk 49 optimal weight:    7.9990
   chunk 92 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 100 optimal weight:    6.9990
   chunk 60 optimal weight:   20.0000
   chunk 83 optimal weight:    1.9990
   overall best weight:    4.1388

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

Flipped N/Q/H residues before XYZ refinement:
2  16 HIS
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  52 ASN
Y  15 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 = 0.3178 r_free = 0.3178 target = 0.047727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.033365 restraints weight = 205703.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.034372 restraints weight = 82625.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.034930 restraints weight = 51986.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.9313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  19762  Z= 0.232
  Angle     :  0.730  27.264  29894  Z= 0.354
  Chirality :  0.047   1.933   3913
  Planarity :  0.005   0.042   1349
  Dihedral  : 25.775 175.440  10573
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 27.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.45 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.35), residues: 507
  helix: -0.18 (0.33), residues: 223
  sheet: -1.65 (0.50), residues: 82
  loop : -1.62 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP T  80 
 HIS   0.004   0.001   HIS Y  41 
 PHE   0.015   0.002   PHE Y  26 
 TYR   0.009   0.002   TYR T  84 
 ARG   0.007   0.001   ARG U  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09096 (  687)
  hydrogen bonds       : angle       4.19939 ( 1350)
  covalent geometry    : bond        0.00428 (19762)
  covalent geometry    : angle       0.72976 (29894)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4573.35 seconds
wall clock time: 81 minutes 21.00 seconds (4881.00 seconds total)