Starting phenix.real_space_refine
on Sat Jul  4 03:00:54 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8c9a_16507/07_2026/8c9a_16507.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c9a_16507/07_2026/8c9a_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_16507/07_2026/8c9a_16507.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c9a_16507/07_2026/8c9a_16507.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8c9a_16507/07_2026/8c9a_16507.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8c9a_16507/07_2026/8c9a_16507.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c9a_16507/07_2026/8c9a_16507.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c9a_16507/07_2026/8c9a_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-dev-6108/lib/python3.11/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: 13
          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: 3.54, per 1000 atoms: 0.20
  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: 1.35
  Conformation dependent library (CDL) restraints added in 308.2 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: 2.48
  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: 3.85

  Time building geometry restraints manager: 1.92 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: 10064
       35.82 -    71.63: 278
       71.63 -   107.45: 43
      107.45 -   143.27: 2
      143.27 -   179.09: 3
  Dihedral angle restraints: 10390
    sinusoidal: 8872
      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 10387 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:             1.810
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.540
  Find NCS groups from input model:        0.050
  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:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
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  : 13.845 179.086   9392
  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 are 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/Z
  covalent geometry    : bond        0.00135 /  0.07 (19762)
  covalent geometry    : angle       0.45142 /  0.21 (29894)
  hydrogen bonds       : bond        0.07736 /  4.48 (  687)
  hydrogen bonds       : angle       4.05371 /  2.56 ( 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  : 0.335 
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: 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: 0.1546
  time to fit residues: 23.2129
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  : 0.317 
-------------------------------------------------------------------------------
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...
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 = 0.3413 r_free = 0.3413 target = 0.057024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.043153 restraints weight = 205933.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.044295 restraints weight = 82017.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.044837 restraints weight = 51654.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.045211 restraints weight = 42212.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.045297 restraints weight = 38190.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  19762  Z= 0.186
  Angle     :  0.644  27.765  29894  Z= 0.308
  Chirality :  0.044   1.957   3913
  Planarity :  0.004   0.053   1349
  Dihedral  : 14.999 169.627   8343
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  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 are not related in a simple way.
  whole:  0.49 (0.37), residues: 507
  helix:  1.24 (0.34), residues: 219
  sheet: -0.32 (0.56), residues: 93
  loop : -0.26 (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   0.016   0.002   PHE Y  26 
 TRP   0.002   0.001   TRP T  80 
 HIS   0.003   0.001   HIS 2  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.19 (19762)
  covalent geometry    : angle       0.64440 /  0.31 (29894)
  hydrogen bonds       : bond        0.07798 /  4.61 (  687)
  hydrogen bonds       : angle       3.80677 /  2.32 ( 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  : 0.304 
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   97 ASN cc_start: 0.8648 (t0) cc_final: 0.7939 (t0)
REVERT: E  163 ASN cc_start: 0.8441 (t0) cc_final: 0.7956 (m-40)
REVERT: E  195 GLN cc_start: 0.9712 (mt0) cc_final: 0.9407 (mt0)
REVERT: E  199 MET cc_start: 0.9003 (mtm) cc_final: 0.8358 (ptp)
REVERT: S   68 ASP cc_start: 0.9462 (t0) cc_final: 0.9226 (t70)
REVERT: U   12 VAL cc_start: 0.8869 (t) cc_final: 0.7804 (t)
REVERT: T   11 LEU cc_start: 0.8711 (pt) cc_final: 0.8412 (pp)
REVERT: T   51 PHE cc_start: 0.8754 (m-80) cc_final: 0.8452 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1518
  time to fit residues: 19.1426
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  : 0.314 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 85 optimal weight:    6.9990
   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:   10.0000
   chunk 46 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    6.9592

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
2  13 ASN
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  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 = 0.3214 r_free = 0.3214 target = 0.049037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.034578 restraints weight = 210240.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.035576 restraints weight = 85216.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 67)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.036115 restraints weight = 55719.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.036353 restraints weight = 46254.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.036399 restraints weight = 42767.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.6361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  19762  Z= 0.387
  Angle     :  0.940  27.503  29894  Z= 0.453
  Chirality :  0.054   1.964   3913
  Planarity :  0.007   0.089   1349
  Dihedral  : 17.891 172.630   8343
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 36.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  5.64 %
    Favored  : 93.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.35), residues: 507
  helix: -0.05 (0.33), residues: 215
  sheet: -1.02 (0.53), residues: 91
  loop : -0.73 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG Y  52 
 TYR   0.023   0.003   TYR T  84 
 PHE   0.027   0.003   PHE Y  26 
 TRP   0.001   0.001   TRP T  80 
 HIS   0.009   0.002   HIS Y  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00716 /  0.39 (19762)
  covalent geometry    : angle       0.93993 /  0.45 (29894)
  hydrogen bonds       : bond        0.12804 /  7.63 (  687)
  hydrogen bonds       : angle       4.75023 /  2.86 ( 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
  78 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   22 MET cc_start: 0.8512 (ttt) cc_final: 0.8308 (ttt)
REVERT: E  102 ARG cc_start: 0.9425 (ptt180) cc_final: 0.9119 (ptp90)
REVERT: E  195 GLN cc_start: 0.9571 (mt0) cc_final: 0.9222 (mt0)
REVERT: E  199 MET cc_start: 0.9187 (mtm) cc_final: 0.8454 (mtm)
REVERT: S   68 ASP cc_start: 0.9476 (t0) cc_final: 0.9229 (t70)
REVERT: T   31 VAL cc_start: 0.9168 (m) cc_final: 0.8875 (t)
REVERT: T   32 LEU cc_start: 0.8776 (mt) cc_final: 0.8462 (mp)
REVERT: T   42 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8569 (pp20)
REVERT: T   87 LEU cc_start: 0.8658 (mt) cc_final: 0.8334 (mt)
  outliers start: 3
  outliers final: 1
  residues processed: 78
  average time/residue: 0.1607
  time to fit residues: 18.2821
Evaluate side-chains
  57 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 87 optimal weight:    1.9990
   chunk 96 optimal weight:    7.9990
   chunk 72 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 99 optimal weight:   10.0000
   chunk 101 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 69 optimal weight:    0.9980
   chunk 52 optimal weight:    9.9990
   overall best weight:    3.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
S  15 GLN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  68 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 = 0.3260 r_free = 0.3260 target = 0.050520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.036682 restraints weight = 206811.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.037372 restraints weight = 121907.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.037344 restraints weight = 74942.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.037329 restraints weight = 67234.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.037355 restraints weight = 61951.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.6162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  19762  Z= 0.204
  Angle     :  0.669  27.085  29894  Z= 0.322
  Chirality :  0.045   1.966   3913
  Planarity :  0.005   0.053   1349
  Dihedral  : 17.317 166.616   8343
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 19.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  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 are not related in a simple way.
  whole: -0.65 (0.35), residues: 507
  helix:  0.31 (0.33), residues: 218
  sheet: -1.07 (0.50), residues: 96
  loop : -0.76 (0.43), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG Y  47 
 TYR   0.009   0.002   TYR T  84 
 PHE   0.018   0.002   PHE Y  26 
 TRP   0.001   0.000   TRP T  80 
 HIS   0.003   0.001   HIS Y  41 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.20 (19762)
  covalent geometry    : angle       0.66897 /  0.32 (29894)
  hydrogen bonds       : bond        0.07752 /  4.61 (  687)
  hydrogen bonds       : angle       4.07883 /  2.49 ( 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
  80 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.252 
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  102 ARG cc_start: 0.9305 (ptt180) cc_final: 0.8934 (ptt-90)
REVERT: E  199 MET cc_start: 0.9241 (mtm) cc_final: 0.8477 (ptp)
REVERT: U    7 ASP cc_start: 0.8973 (m-30) cc_final: 0.8694 (m-30)
REVERT: U   52 ASN cc_start: 0.9142 (t0) cc_final: 0.8923 (p0)
REVERT: T   31 VAL cc_start: 0.8911 (m) cc_final: 0.8658 (t)
REVERT: T   32 LEU cc_start: 0.8741 (mt) cc_final: 0.8440 (mt)
REVERT: T   51 PHE cc_start: 0.8815 (m-80) cc_final: 0.8477 (m-80)
REVERT: T   87 LEU cc_start: 0.8299 (mt) cc_final: 0.7976 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1534
  time to fit residues: 18.2023
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  : 0.314 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 97 optimal weight:    5.9990
   chunk 96 optimal weight:   10.0000
   chunk 60 optimal weight:   20.0000
   chunk 80 optimal weight:    6.9990
   chunk 69 optimal weight:    0.0770
   chunk 52 optimal weight:   10.0000
   chunk 108 optimal weight:   20.0000
   chunk 43 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   overall best weight:    6.4148

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  61 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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.047918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.033438 restraints weight = 212439.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.034299 restraints weight = 90427.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.034803 restraints weight = 59144.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.034972 restraints weight = 49360.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.035098 restraints weight = 46336.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.7746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053  19762  Z= 0.357
  Angle     :  0.887  27.306  29894  Z= 0.427
  Chirality :  0.053   1.933   3913
  Planarity :  0.007   0.084   1349
  Dihedral  : 18.712 178.798   8343
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 36.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    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 are not related in a simple way.
  whole: -1.48 (0.34), residues: 507
  helix: -0.50 (0.30), residues: 221
  sheet: -1.60 (0.50), residues: 96
  loop : -0.95 (0.42), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG U  81 
 TYR   0.015   0.002   TYR T  84 
 PHE   0.018   0.003   PHE U  94 
 TRP   0.000   0.000   TRP T  80 
 HIS   0.005   0.002   HIS E 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00658 /  0.36 (19762)
  covalent geometry    : angle       0.88668 /  0.43 (29894)
  hydrogen bonds       : bond        0.12058 /  7.22 (  687)
  hydrogen bonds       : angle       4.61601 /  2.79 ( 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
  75 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.368 
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   30 GLN cc_start: 0.9379 (mt0) cc_final: 0.9121 (mt0)
REVERT: E  102 ARG cc_start: 0.9359 (ptt180) cc_final: 0.9137 (ptt90)
REVERT: E  144 GLU cc_start: 0.8489 (mp0) cc_final: 0.8284 (mp0)
REVERT: E  184 ASP cc_start: 0.9221 (t0) cc_final: 0.8859 (t0)
REVERT: E  199 MET cc_start: 0.9295 (mtm) cc_final: 0.8703 (mtm)
REVERT: Y    4 LYS cc_start: 0.9271 (pttm) cc_final: 0.8868 (pptt)
REVERT: Y   30 MET cc_start: 0.8750 (mmm) cc_final: 0.8474 (tpp)
REVERT: T   31 VAL cc_start: 0.9257 (m) cc_final: 0.8883 (t)
REVERT: T   32 LEU cc_start: 0.8546 (mt) cc_final: 0.8240 (mp)
REVERT: T   87 LEU cc_start: 0.8593 (mt) cc_final: 0.8258 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1649
  time to fit residues: 17.7724
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  : 0.337 
-------------------------------------------------------------------------------
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:   10.9990
   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:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 33 optimal weight:    8.9990
   chunk 34 optimal weight:    9.9990
   overall best weight:    8.1992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  31 GLN
S  60 HIS
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 = 0.3128 r_free = 0.3128 target = 0.046517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.031946 restraints weight = 214663.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.032811 restraints weight = 94219.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.033252 restraints weight = 63616.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.033518 restraints weight = 53983.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.033551 restraints weight = 49664.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.9439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.048  19762  Z= 0.428
  Angle     :  0.994  27.044  29894  Z= 0.484
  Chirality :  0.057   1.928   3913
  Planarity :  0.007   0.081   1349
  Dihedral  : 20.259 171.631   8343
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 45.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  4.51 %
    Favored  : 95.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.26 (0.33), residues: 507
  helix: -1.02 (0.30), residues: 221
  sheet: -1.80 (0.54), residues: 81
  loop : -1.73 (0.39), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG U  81 
 TYR   0.019   0.003   TYR T  84 
 PHE   0.035   0.004   PHE 2  18 
 TRP   0.002   0.001   TRP T  80 
 HIS   0.006   0.002   HIS E 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00794 /  0.43 (19762)
  covalent geometry    : angle       0.99391 /  0.48 (29894)
  hydrogen bonds       : bond        0.13374 /  7.98 (  687)
  hydrogen bonds       : angle       5.09435 /  3.09 ( 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
  73 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.326 
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: 0.8630 (ttt) cc_final: 0.8355 (ttt)
REVERT: E   16 GLU cc_start: 0.9415 (tm-30) cc_final: 0.9205 (tp30)
REVERT: E   30 GLN cc_start: 0.9455 (mt0) cc_final: 0.9190 (mt0)
REVERT: E  184 ASP cc_start: 0.9079 (t0) cc_final: 0.8683 (t0)
REVERT: E  199 MET cc_start: 0.9354 (mtm) cc_final: 0.8488 (mtm)
REVERT: U   52 ASN cc_start: 0.8846 (t0) cc_final: 0.8634 (p0)
REVERT: T   31 VAL cc_start: 0.9205 (m) cc_final: 0.8516 (t)
REVERT: T   32 LEU cc_start: 0.8513 (mt) cc_final: 0.8234 (mp)
REVERT: T   87 LEU cc_start: 0.8771 (mt) cc_final: 0.8469 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 73
  average time/residue: 0.1561
  time to fit residues: 16.5570
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  : 0.316 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 53 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 35 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   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:    7.7994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3128 r_free = 0.3128 target = 0.047119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.033415 restraints weight = 222338.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.034395 restraints weight = 88887.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.034927 restraints weight = 55879.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.035094 restraints weight = 45677.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.035211 restraints weight = 42731.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.9756

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= 0.401
  Angle     :  0.936  27.188  29894  Z= 0.452
  Chirality :  0.055   1.923   3913
  Planarity :  0.007   0.053   1349
  Dihedral  : 20.306 174.153   8343
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 42.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    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 are not related in a simple way.
  whole: -2.42 (0.33), residues: 507
  helix: -1.00 (0.31), residues: 222
  sheet: -2.16 (0.48), residues: 89
  loop : -1.84 (0.41), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E 102 
 TYR   0.012   0.003   TYR T  84 
 PHE   0.023   0.003   PHE 2  18 
 TRP   0.001   0.001   TRP T  80 
 HIS   0.005   0.002   HIS E 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00742 /  0.40 (19762)
  covalent geometry    : angle       0.93592 /  0.45 (29894)
  hydrogen bonds       : bond        0.12669 /  7.52 (  687)
  hydrogen bonds       : angle       4.88848 /  2.94 ( 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
  68 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   22 MET cc_start: 0.8650 (ttt) cc_final: 0.8348 (ttt)
REVERT: E  195 GLN cc_start: 0.9606 (mt0) cc_final: 0.9140 (mt0)
REVERT: E  199 MET cc_start: 0.9382 (mtm) cc_final: 0.8515 (mtm)
REVERT: U   52 ASN cc_start: 0.8900 (t0) cc_final: 0.8660 (p0)
REVERT: T   80 TRP cc_start: 0.7326 (p-90) cc_final: 0.7066 (p-90)
REVERT: T   87 LEU cc_start: 0.8987 (mt) cc_final: 0.8693 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1346
  time to fit residues: 13.5444
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  : 0.231 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 13 optimal weight:   10.0000
   chunk 24 optimal weight:    8.9990
   chunk 36 optimal weight:    9.9990
   chunk 18 optimal weight:   20.0000
   chunk 114 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    7.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
S  15 GLN
U  68 ASN
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 = 0.3121 r_free = 0.3121 target = 0.046931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.033495 restraints weight = 222409.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.034302 restraints weight = 88855.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.034845 restraints weight = 55313.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.035098 restraints weight = 45186.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.035168 restraints weight = 41432.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          1.0226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064  19762  Z= 0.390
  Angle     :  0.935  27.165  29894  Z= 0.452
  Chirality :  0.055   1.925   3913
  Planarity :  0.006   0.053   1349
  Dihedral  : 20.612 177.701   8343
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 43.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.13 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.34), residues: 507
  helix: -0.95 (0.32), residues: 222
  sheet: -2.10 (0.50), residues: 87
  loop : -2.10 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG U  81 
 TYR   0.011   0.003   TYR T  84 
 PHE   0.019   0.003   PHE Y  26 
 TRP   0.002   0.001   TRP T  80 
 HIS   0.005   0.002   HIS 2  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00725 /  0.39 (19762)
  covalent geometry    : angle       0.93550 /  0.45 (29894)
  hydrogen bonds       : bond        0.12644 /  7.48 (  687)
  hydrogen bonds       : angle       4.80318 /  2.91 ( 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
  73 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   22 MET cc_start: 0.8873 (ttt) cc_final: 0.8559 (ttt)
REVERT: E  100 MET cc_start: 0.9236 (mtt) cc_final: 0.8901 (mtp)
REVERT: E  102 ARG cc_start: 0.9167 (mtm-85) cc_final: 0.8936 (mtm-85)
REVERT: E  195 GLN cc_start: 0.9633 (mt0) cc_final: 0.9165 (mt0)
REVERT: E  199 MET cc_start: 0.9388 (mtm) cc_final: 0.8591 (mtm)
REVERT: U   52 ASN cc_start: 0.8885 (t0) cc_final: 0.8659 (p0)
REVERT: T   32 LEU cc_start: 0.8444 (mt) cc_final: 0.8135 (mp)
REVERT: T   87 LEU cc_start: 0.9140 (mt) cc_final: 0.8828 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1580
  time to fit residues: 16.7801
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  : 0.306 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 75 optimal weight:    0.6980
   chunk 43 optimal weight:   10.0000
   chunk 72 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 19 optimal weight:   10.0000
   overall best weight:    6.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
2  16 HIS
** S  15 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 = 0.3136 r_free = 0.3136 target = 0.047304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.033759 restraints weight = 216470.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.034749 restraints weight = 85589.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.035312 restraints weight = 53281.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.035499 restraints weight = 43007.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.035640 restraints weight = 39970.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          1.0249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  19762  Z= 0.335
  Angle     :  0.855  27.181  29894  Z= 0.413
  Chirality :  0.052   1.931   3913
  Planarity :  0.006   0.060   1349
  Dihedral  : 20.272 179.889   8343
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 37.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  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 are not related in a simple way.
  whole: -2.42 (0.34), residues: 507
  helix: -0.77 (0.32), residues: 223
  sheet: -2.62 (0.43), residues: 100
  loop : -1.80 (0.41), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 102 
 TYR   0.010   0.002   TYR T  84 
 PHE   0.019   0.003   PHE Y  26 
 TRP   0.001   0.000   TRP T  80 
 HIS   0.004   0.001   HIS 2  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00621 /  0.34 (19762)
  covalent geometry    : angle       0.85462 /  0.41 (29894)
  hydrogen bonds       : bond        0.11342 /  6.70 (  687)
  hydrogen bonds       : angle       4.57918 /  2.75 ( 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
  74 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.279 
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: 0.8801 (ttt) cc_final: 0.8520 (ttt)
REVERT: E  100 MET cc_start: 0.9371 (mtt) cc_final: 0.8963 (mtp)
REVERT: E  199 MET cc_start: 0.9259 (mtm) cc_final: 0.8443 (mtm)
REVERT: U   52 ASN cc_start: 0.8889 (t0) cc_final: 0.8664 (p0)
REVERT: T    1 MET cc_start: 0.6671 (pmm) cc_final: 0.6394 (pmm)
REVERT: T   11 LEU cc_start: 0.8961 (pt) cc_final: 0.8755 (pp)
REVERT: T   31 VAL cc_start: 0.9172 (m) cc_final: 0.8571 (t)
REVERT: T   32 LEU cc_start: 0.8377 (mt) cc_final: 0.7972 (mp)
REVERT: T   51 PHE cc_start: 0.8821 (m-80) cc_final: 0.8588 (m-80)
REVERT: T   80 TRP cc_start: 0.7133 (p-90) cc_final: 0.6916 (p-90)
REVERT: T   87 LEU cc_start: 0.9168 (mt) cc_final: 0.8863 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1453
  time to fit residues: 15.8049
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  : 0.300 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 64 optimal weight:   30.0000
   chunk 6 optimal weight:    6.9990
   chunk 78 optimal weight:    8.9990
   chunk 0 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 81 optimal weight:    5.9990
   chunk 96 optimal weight:    0.8980
   chunk 90 optimal weight:   10.0000
   chunk 86 optimal weight:    8.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    4.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** S  15 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.047948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.034484 restraints weight = 213747.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.035398 restraints weight = 83630.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.035983 restraints weight = 51565.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.036249 restraints weight = 41602.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2753 r_free = 0.2753 target = 0.036317 restraints weight = 38095.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          1.0145

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= 0.270
  Angle     :  0.776  27.080  29894  Z= 0.375
  Chirality :  0.049   1.943   3913
  Planarity :  0.005   0.045   1349
  Dihedral  : 19.865 176.004   8343
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 31.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  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 are not related in a simple way.
  whole: -2.08 (0.34), residues: 507
  helix: -0.59 (0.32), residues: 223
  sheet: -1.80 (0.54), residues: 71
  loop : -2.00 (0.38), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG U  81 
 TYR   0.008   0.002   TYR T  84 
 PHE   0.018   0.002   PHE Y  26 
 TRP   0.002   0.001   TRP T  80 
 HIS   0.004   0.001   HIS S  60 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00500 /  0.27 (19762)
  covalent geometry    : angle       0.77636 /  0.37 (29894)
  hydrogen bonds       : bond        0.09736 /  5.77 (  687)
  hydrogen bonds       : angle       4.34911 /  2.60 ( 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
  73 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.319 
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: 0.9301 (mtt) cc_final: 0.8852 (mtp)
REVERT: E  199 MET cc_start: 0.9313 (mtm) cc_final: 0.8318 (mtm)
REVERT: U   52 ASN cc_start: 0.8841 (t0) cc_final: 0.8625 (p0)
REVERT: T    1 MET cc_start: 0.6784 (pmm) cc_final: 0.6526 (pmm)
REVERT: T   11 LEU cc_start: 0.8868 (pt) cc_final: 0.8667 (pp)
REVERT: T   31 VAL cc_start: 0.9191 (m) cc_final: 0.8680 (t)
REVERT: T   32 LEU cc_start: 0.8382 (mt) cc_final: 0.7974 (mt)
REVERT: T   51 PHE cc_start: 0.8855 (m-80) cc_final: 0.8619 (m-80)
REVERT: T   87 LEU cc_start: 0.9179 (mt) cc_final: 0.8879 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1331
  time to fit residues: 14.4427
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  : 0.300 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 105 optimal weight:    4.9990
   chunk 80 optimal weight:    6.9990
   chunk 64 optimal weight:   30.0000
   chunk 18 optimal weight:   20.0000
   chunk 21 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 1 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 28 optimal weight:    8.9990
   chunk 91 optimal weight:    0.8980
   overall best weight:    4.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.048095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.034575 restraints weight = 215467.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.035586 restraints weight = 83639.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.036170 restraints weight = 51853.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.036459 restraints weight = 41895.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.036549 restraints weight = 38086.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          1.0171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  19762  Z= 0.256
  Angle     :  0.758  27.109  29894  Z= 0.366
  Chirality :  0.048   1.943   3913
  Planarity :  0.005   0.063   1349
  Dihedral  : 19.679 176.885   8343
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 29.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.34), residues: 507
  helix: -0.50 (0.32), residues: 224
  sheet: -1.83 (0.54), residues: 71
  loop : -2.05 (0.38), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG U  81 
 TYR   0.010   0.002   TYR S  38 
 PHE   0.018   0.002   PHE Y  26 
 TRP   0.002   0.001   TRP T  80 
 HIS   0.003   0.001   HIS E 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00474 /  0.26 (19762)
  covalent geometry    : angle       0.75847 /  0.37 (29894)
  hydrogen bonds       : bond        0.09467 /  5.61 (  687)
  hydrogen bonds       : angle       4.29173 /  2.53 ( 1350)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2451.52 seconds
wall clock time: 43 minutes 49.69 seconds (2629.69 seconds total)