Starting phenix.real_space_refine
on Tue Nov 19 00:07:00 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/11_2024/8c9a_16507.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/11_2024/8c9a_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/11_2024/8c9a_16507.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/11_2024/8c9a_16507.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/11_2024/8c9a_16507.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c9a_16507/11_2024/8c9a_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-5513/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: 10.21, 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: 4.48
  Conformation dependent library (CDL) restraints added in 793.3 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: 8.22
  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: 9.72

  Time building geometry restraints manager: 5.23 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:             2.060
  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:          0.590
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     47.070
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.070
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.310
-------------------------------------------------------------------------------
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= 0.082
  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 

*********************** 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  : 0.942 
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: 0.3577
  time to fit residues: 52.3224
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  : 0.885 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
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= 0.319
  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 

*********************** 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  : 0.961 
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: 0.8693 (t0) cc_final: 0.8028 (t0)
REVERT: E  100 MET cc_start: 0.9363 (mtt) cc_final: 0.9156 (mtt)
REVERT: E  163 ASN cc_start: 0.8448 (t0) cc_final: 0.7962 (m-40)
REVERT: E  188 MET cc_start: 0.8859 (ttt) cc_final: 0.8444 (tpt)
REVERT: E  199 MET cc_start: 0.9110 (mtm) cc_final: 0.8491 (ptp)
REVERT: S   68 ASP cc_start: 0.9485 (t0) cc_final: 0.9272 (t70)
REVERT: U   17 ASP cc_start: 0.7727 (t0) cc_final: 0.7474 (t0)
REVERT: T   11 LEU cc_start: 0.8694 (pt) cc_final: 0.8355 (pp)
REVERT: T   51 PHE cc_start: 0.8833 (m-80) cc_final: 0.8529 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 82
  average time/residue: 0.3321
  time to fit residues: 40.7442
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  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 58 optimal weight:   30.0000
   chunk 32 optimal weight:    8.9990
   chunk 86 optimal weight:    5.9990
   chunk 71 optimal weight:    8.9990
   chunk 28 optimal weight:    6.9990
   chunk 104 optimal weight:    8.9990
   chunk 113 optimal weight:    0.0670
   chunk 93 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   chunk 35 optimal weight:    9.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    3.8124

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.4944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  19762  Z= 0.241
  Angle     :  0.664  26.919  29894  Z= 0.319
  Chirality :  0.045   1.950   3913
  Planarity :  0.005   0.070   1349
  Dihedral  : 24.651 167.764  10573
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 20.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.10 (0.36), residues: 507
  helix:  0.71 (0.33), residues: 219
  sheet: -0.57 (0.54), residues: 91
  loop : -0.55 (0.43), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP T  80 
 HIS   0.004   0.001   HIS Y  41 
 PHE   0.027   0.002   PHE E  23 
 TYR   0.013   0.002   TYR T  84 
 ARG   0.004   0.001   ARG T   3 

*********************** 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
  81 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.922 
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   25 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8977 (tm-30)
REVERT: E  149 ILE cc_start: 0.9539 (tp) cc_final: 0.8378 (tp)
REVERT: E  195 GLN cc_start: 0.9737 (mt0) cc_final: 0.9368 (mt0)
REVERT: E  199 MET cc_start: 0.9191 (mtm) cc_final: 0.8397 (ptp)
REVERT: U    7 ASP cc_start: 0.8347 (m-30) cc_final: 0.8135 (m-30)
REVERT: T   32 LEU cc_start: 0.8847 (mt) cc_final: 0.8630 (mt)
REVERT: T   51 PHE cc_start: 0.8844 (m-80) cc_final: 0.8479 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.3495
  time to fit residues: 41.7934
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  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   chunk 54 optimal weight:   10.0000
   chunk 11 optimal weight:   10.0000
   chunk 49 optimal weight:    8.9990
   chunk 70 optimal weight:    7.9990
   chunk 104 optimal weight:    9.9990
   chunk 111 optimal weight:    3.9990
   chunk 99 optimal weight:   20.0000
   chunk 29 optimal weight:    8.9990
   chunk 92 optimal weight:    7.9990
   overall best weight:    5.5988

-------------------------------------------------------------------------------
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**
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.6799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  19762  Z= 0.353
  Angle     :  0.837  27.658  29894  Z= 0.404
  Chirality :  0.051   1.932   3913
  Planarity :  0.006   0.064   1349
  Dihedral  : 25.356 174.238  10573
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 31.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.31 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    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 (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: -1.01 (0.35), residues: 507
  helix: -0.03 (0.32), residues: 217
  sheet: -1.31 (0.50), residues: 96
  loop : -0.85 (0.43), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP T  80 
 HIS   0.006   0.001   HIS Y  41 
 PHE   0.020   0.003   PHE Y  26 
 TYR   0.017   0.003   TYR T  84 
 ARG   0.014   0.001   ARG E 102 

*********************** 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: 0
    poor density    : 80
  time to evaluate  : 0.994 
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: 0.9238 (tm-30) cc_final: 0.9024 (tm-30)
REVERT: E  100 MET cc_start: 0.9314 (mtt) cc_final: 0.8819 (mtp)
REVERT: E  199 MET cc_start: 0.9347 (mtm) cc_final: 0.8642 (mtp)
REVERT: S   68 ASP cc_start: 0.9564 (t0) cc_final: 0.9351 (t0)
REVERT: U    7 ASP cc_start: 0.8810 (m-30) cc_final: 0.8593 (m-30)
REVERT: T   32 LEU cc_start: 0.8637 (mt) cc_final: 0.8376 (mp)
REVERT: T   87 LEU cc_start: 0.8468 (mt) cc_final: 0.8182 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.3660
  time to fit residues: 42.4343
Evaluate side-chains
  55 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 63 optimal weight:   20.0000
   chunk 1 optimal weight:   10.0000
   chunk 82 optimal weight:    9.9990
   chunk 45 optimal weight:   10.0000
   chunk 94 optimal weight:    0.8980
   chunk 76 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:   20.0000
   chunk 99 optimal weight:    0.2980
   chunk 28 optimal weight:    7.9990
   chunk 37 optimal weight:   20.0000
   overall best weight:    5.4386

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

Flipped N/Q/H residues before XYZ refinement:
S  15 GLN
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: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.7468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  19762  Z= 0.319
  Angle     :  0.773  27.191  29894  Z= 0.373
  Chirality :  0.049   1.930   3913
  Planarity :  0.006   0.069   1349
  Dihedral  : 25.464 176.654  10573
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 29.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  4.06 %
    Favored  : 95.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.30 (0.34), residues: 507
  helix: -0.26 (0.32), residues: 221
  sheet: -1.57 (0.49), residues: 96
  loop : -0.97 (0.42), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP T  80 
 HIS   0.005   0.001   HIS Y  41 
 PHE   0.016   0.002   PHE Y  26 
 TYR   0.015   0.002   TYR T  84 
 ARG   0.008   0.001   ARG Y  47 

*********************** 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
  80 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 79
  time to evaluate  : 0.964 
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: 0.8491 (ttt) cc_final: 0.8218 (ttt)
REVERT: E   25 GLU cc_start: 0.9267 (tm-30) cc_final: 0.9037 (tm-30)
REVERT: E  102 ARG cc_start: 0.9222 (mtm-85) cc_final: 0.8913 (mtm110)
REVERT: E  199 MET cc_start: 0.9348 (mtm) cc_final: 0.8517 (ptp)
REVERT: U    7 ASP cc_start: 0.8771 (m-30) cc_final: 0.8558 (m-30)
REVERT: T   32 LEU cc_start: 0.8594 (mt) cc_final: 0.8333 (mp)
  outliers start: 1
  outliers final: 0
  residues processed: 80
  average time/residue: 0.3714
  time to fit residues: 42.5852
Evaluate side-chains
  59 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 100 optimal weight:    4.9990
   chunk 21 optimal weight:    9.9990
   chunk 65 optimal weight:    8.9990
   chunk 27 optimal weight:   10.0000
   chunk 111 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   chunk 51 optimal weight:   20.0000
   chunk 9 optimal weight:    7.9990
   chunk 36 optimal weight:   20.0000
   chunk 58 optimal weight:   30.0000
   chunk 107 optimal weight:    8.9990
   overall best weight:    5.3990

-------------------------------------------------------------------------------
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**
U  68 ASN
Y  15 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.8203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035  19762  Z= 0.327
  Angle     :  0.800  27.201  29894  Z= 0.388
  Chirality :  0.050   1.922   3913
  Planarity :  0.006   0.100   1349
  Dihedral  : 25.703 178.827  10573
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 31.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.37 (0.34), residues: 507
  helix: -0.24 (0.32), residues: 220
  sheet: -1.32 (0.51), residues: 83
  loop : -1.32 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP T  80 
 HIS   0.005   0.001   HIS Y  41 
 PHE   0.020   0.003   PHE 2  18 
 TYR   0.014   0.002   TYR T  84 
 ARG   0.009   0.001   ARG Y  47 

*********************** 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
  72 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   22 MET cc_start: 0.8605 (ttt) cc_final: 0.8284 (ttt)
REVERT: E   25 GLU cc_start: 0.9244 (tm-30) cc_final: 0.9033 (tm-30)
REVERT: E  100 MET cc_start: 0.9224 (mtt) cc_final: 0.8725 (mtp)
REVERT: E  117 ARG cc_start: 0.6071 (mtp180) cc_final: 0.4832 (mtp180)
REVERT: E  199 MET cc_start: 0.9363 (mtm) cc_final: 0.8948 (mtm)
REVERT: Y    7 ARG cc_start: 0.9100 (ptp-110) cc_final: 0.8800 (ptp-110)
REVERT: T   87 LEU cc_start: 0.8460 (mt) cc_final: 0.8153 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.3852
  time to fit residues: 39.7743
Evaluate side-chains
  51 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 63 optimal weight:   20.0000
   chunk 81 optimal weight:    6.9990
   chunk 62 optimal weight:   30.0000
   chunk 93 optimal weight:    4.9990
   chunk 110 optimal weight:    1.9990
   chunk 69 optimal weight:   10.0000
   chunk 67 optimal weight:    6.9990
   chunk 51 optimal weight:   20.0000
   chunk 68 optimal weight:    9.9990
   chunk 44 optimal weight:   10.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
E 136 GLN
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  68 ASN
Y  15 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.9025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  19762  Z= 0.367
  Angle     :  0.856  27.382  29894  Z= 0.414
  Chirality :  0.052   1.922   3913
  Planarity :  0.007   0.103   1349
  Dihedral  : 25.978 178.378  10573
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 35.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    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: -1.78 (0.34), residues: 507
  helix: -0.46 (0.33), residues: 222
  sheet: -1.30 (0.55), residues: 73
  loop : -1.83 (0.38), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP T  80 
 HIS   0.005   0.002   HIS E 165 
 PHE   0.021   0.003   PHE 2  18 
 TYR   0.016   0.003   TYR T  84 
 ARG   0.007   0.001   ARG U  81 

*********************** 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  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 GLU cc_start: 0.9280 (tm-30) cc_final: 0.8995 (tm-30)
REVERT: E   27 LEU cc_start: 0.9581 (mt) cc_final: 0.9362 (mt)
REVERT: E  100 MET cc_start: 0.9120 (mtt) cc_final: 0.8705 (mtp)
REVERT: E  199 MET cc_start: 0.9472 (mtm) cc_final: 0.8939 (mtm)
REVERT: Y    7 ARG cc_start: 0.9106 (ptp-110) cc_final: 0.8828 (ptp-110)
REVERT: T   32 LEU cc_start: 0.8546 (mt) cc_final: 0.8234 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.3870
  time to fit residues: 37.4639
Evaluate side-chains
  48 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 21 optimal weight:    9.9990
   chunk 70 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 54 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   chunk 100 optimal weight:   10.0000
   chunk 106 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
2  16 HIS
E  30 GLN
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  68 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.8875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  19762  Z= 0.271
  Angle     :  0.740  27.207  29894  Z= 0.359
  Chirality :  0.048   1.930   3913
  Planarity :  0.006   0.078   1349
  Dihedral  : 25.715 175.737  10573
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 28.03
  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 (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: -1.58 (0.35), residues: 507
  helix: -0.25 (0.33), residues: 223
  sheet: -1.53 (0.50), residues: 82
  loop : -1.63 (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 2  18 
 TYR   0.010   0.002   TYR T  84 
 ARG   0.006   0.001   ARG Y  23 

*********************** 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
  70 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   22 MET cc_start: 0.8570 (ttt) cc_final: 0.8304 (ttt)
REVERT: E   25 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8949 (tm-30)
REVERT: E   30 GLN cc_start: 0.9445 (mt0) cc_final: 0.9241 (mt0)
REVERT: E  100 MET cc_start: 0.9193 (mtt) cc_final: 0.8619 (mtp)
REVERT: E  199 MET cc_start: 0.9336 (mtm) cc_final: 0.8646 (ptm)
REVERT: U    7 ASP cc_start: 0.8730 (m-30) cc_final: 0.8528 (m-30)
REVERT: T   32 LEU cc_start: 0.8436 (mt) cc_final: 0.8123 (mp)
REVERT: T   51 PHE cc_start: 0.8819 (m-80) cc_final: 0.8535 (m-80)
REVERT: T   87 LEU cc_start: 0.8650 (mt) cc_final: 0.8396 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.3880
  time to fit residues: 38.9444
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  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 62 optimal weight:   30.0000
   chunk 44 optimal weight:   10.0000
   chunk 81 optimal weight:    6.9990
   chunk 31 optimal weight:    8.9990
   chunk 93 optimal weight:    8.9990
   chunk 97 optimal weight:    0.5980
   chunk 102 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9990
   chunk 109 optimal weight:    0.0570
   overall best weight:    1.3304

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.8026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  19762  Z= 0.141
  Angle     :  0.611  27.117  29894  Z= 0.293
  Chirality :  0.043   1.954   3913
  Planarity :  0.004   0.036   1349
  Dihedral  : 24.943 164.873  10573
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 16.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  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 (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: -1.02 (0.35), residues: 507
  helix:  0.35 (0.34), residues: 218
  sheet: -1.20 (0.50), residues: 83
  loop : -1.48 (0.41), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP T  80 
 HIS   0.003   0.001   HIS E  29 
 PHE   0.019   0.002   PHE U  95 
 TYR   0.009   0.002   TYR S  38 
 ARG   0.003   0.000   ARG 2  14 

*********************** 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
  77 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  100 MET cc_start: 0.9175 (mtt) cc_final: 0.8741 (mtp)
REVERT: E  199 MET cc_start: 0.9171 (mtm) cc_final: 0.8698 (ptp)
REVERT: T   51 PHE cc_start: 0.8684 (m-80) cc_final: 0.8375 (m-80)
REVERT: T   80 TRP cc_start: 0.7165 (p-90) cc_final: 0.6898 (p-90)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.4171
  time to fit residues: 45.5803
Evaluate side-chains
  49 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 51 optimal weight:   20.0000
   chunk 75 optimal weight:    5.9990
   chunk 114 optimal weight:    8.9990
   chunk 105 optimal weight:    7.9990
   chunk 91 optimal weight:    0.6980
   chunk 9 optimal weight:    8.9990
   chunk 70 optimal weight:    9.9990
   chunk 55 optimal weight:   20.0000
   chunk 72 optimal weight:    9.9990
   chunk 97 optimal weight:    0.0050
   overall best weight:    3.3400

-------------------------------------------------------------------------------
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  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.8375

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= 0.217
  Angle     :  0.659  27.135  29894  Z= 0.318
  Chirality :  0.044   1.933   3913
  Planarity :  0.005   0.057   1349
  Dihedral  : 25.202 171.155  10573
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 21.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  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 (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: -1.04 (0.35), residues: 507
  helix:  0.33 (0.34), residues: 218
  sheet: -1.07 (0.56), residues: 70
  loop : -1.57 (0.39), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP T  80 
 HIS   0.003   0.001   HIS S  60 
 PHE   0.013   0.002   PHE U  95 
 TYR   0.008   0.002   TYR T  84 
 ARG   0.005   0.001   ARG Y   7 

********************** 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
  74 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   16 GLU cc_start: 0.9272 (tm-30) cc_final: 0.9038 (tm-30)
REVERT: E  100 MET cc_start: 0.9281 (mtt) cc_final: 0.8687 (mtp)
REVERT: E  199 MET cc_start: 0.9291 (mtm) cc_final: 0.8402 (mtm)
REVERT: U    7 ASP cc_start: 0.8513 (m-30) cc_final: 0.8295 (m-30)
REVERT: Y    7 ARG cc_start: 0.8954 (ptp90) cc_final: 0.8362 (ttp80)
REVERT: T   11 LEU cc_start: 0.8869 (pt) cc_final: 0.8638 (pp)
REVERT: T   29 THR cc_start: 0.7954 (m) cc_final: 0.7690 (m)
REVERT: T   32 LEU cc_start: 0.8593 (mt) cc_final: 0.8387 (mp)
REVERT: T   51 PHE cc_start: 0.8772 (m-80) cc_final: 0.8497 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.3848
  time to fit residues: 40.5468
Evaluate side-chains
  49 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 84 optimal weight:    7.9990
   chunk 13 optimal weight:   10.0000
   chunk 25 optimal weight:    9.9990
   chunk 91 optimal weight:    0.9980
   chunk 38 optimal weight:   10.0000
   chunk 93 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 16 optimal weight:    8.9990
   chunk 80 optimal weight:    0.8980
   chunk 5 optimal weight:    9.9990
   overall best weight:    5.1786

-------------------------------------------------------------------------------
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  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 = 0.3185 r_free = 0.3185 target = 0.048817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.034969 restraints weight = 214457.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.035994 restraints weight = 83308.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 66)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.036579 restraints weight = 52339.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.9017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  19762  Z= 0.308
  Angle     :  0.759  27.227  29894  Z= 0.368
  Chirality :  0.048   1.926   3913
  Planarity :  0.006   0.078   1349
  Dihedral  : 25.620 176.353  10573
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 29.32
  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: -1.39 (0.35), residues: 507
  helix:  0.02 (0.34), residues: 222
  sheet: -1.26 (0.55), residues: 69
  loop : -1.76 (0.39), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP T  80 
 HIS   0.003   0.001   HIS S   9 
 PHE   0.018   0.002   PHE 2  18 
 TYR   0.011   0.002   TYR T  84 
 ARG   0.007   0.001   ARG Y  47 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2256.93 seconds
wall clock time: 43 minutes 49.86 seconds (2629.86 seconds total)