Starting phenix.real_space_refine
on Mon May 19 03:33:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c9a_16507/05_2025/8c9a_16507.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c9a_16507/05_2025/8c9a_16507.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c9a_16507/05_2025/8c9a_16507.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c9a_16507/05_2025/8c9a_16507.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c9a_16507/05_2025/8c9a_16507.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c9a_16507/05_2025/8c9a_16507.cif"
  }
  resolution = 4.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     650      5.49       5
     S      10      5.16       5
     C    8805      2.51       5
     N    3358      2.21       5
     O    5236      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 10.35, 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: 4.18
  Conformation dependent library (CDL) restraints added in 790.2 milliseconds
  

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

  Finding SS restraints...
Warning! N1 atom is missing from residue    G A 356  
  Was trying to link:    G A 356 N1 with    U A 284 O4, Saenger class: 27
Warning! N1 atom is missing from residue    G A 356  
  Was trying to link:    G A 356 N1 with    U A 284 O2, Saenger class: 28
    Secondary structure from input PDB file:
      19 helices and 5 sheets defined
      44.6% alpha, 14.7% beta
      198 base pairs and 310 stacking pairs defined.
    Time for finding SS restraints: 8.49
  Creating SS restraints...
    Processing helix  chain '2' and resid 10 through 17
    Processing helix  chain '2' and resid 17 through 24
      removed outlier: 4.282A  pdb=" N   THR 2  24 " --> pdb=" O   ALA 2  20 " (cutoff:3.500A)
    Processing helix  chain '2' and resid 24 through 38
    Processing helix  chain 'E' and resid 15 through 20
    Processing helix  chain 'E' and resid 24 through 38
    Processing helix  chain 'E' and resid 97 through 115
    Processing helix  chain 'E' and resid 130 through 141
      removed outlier: 3.689A  pdb=" N   LEU E 134 " --> pdb=" O   LYS E 130 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   MET E 141 " --> pdb=" O   LYS E 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 154 through 162
    Processing helix  chain 'E' and resid 176 through 183
      removed outlier: 3.566A  pdb=" N   PHE E 183 " --> pdb=" O   SER E 179 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 190 through 201
    Processing helix  chain 'S' and resid 13 through 22
    Processing helix  chain 'S' and resid 28 through 38
      removed outlier: 4.349A  pdb=" N   TYR S  38 " --> pdb=" O   ASP S  34 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 41 through 63
      removed outlier: 3.789A  pdb=" N   VAL S  45 " --> pdb=" O   LYS S  41 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU S  46 " --> pdb=" O   LYS S  42 " (cutoff:3.500A)
    Processing helix  chain 'U' and resid 65 through 67
      No H-bonds generated for 'chain 'U' and resid 65 through 67'
    Processing helix  chain 'Y' and resid 9 through 35
      removed outlier: 3.525A  pdb=" N   GLU Y  13 " --> pdb=" O   LYS Y   9 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLN Y  25 " --> pdb=" O   LEU Y  21 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   PHE Y  26 " --> pdb=" O   LEU Y  22 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 40 through 56
      removed outlier: 3.817A  pdb=" N   LYS Y  44 " --> pdb=" O   SER Y  40 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU Y  56 " --> pdb=" O   ARG Y  52 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 4 through 9
      removed outlier: 3.531A  pdb=" N   LEU T   8 " --> pdb=" O   GLU T   4 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 17 through 27
      removed outlier: 3.847A  pdb=" N   GLU T  25 " --> pdb=" O   SER T  21 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 39 through 52
    Processing sheet with id=AA1, first strand: chain 'E' and resid 118 through 121
      removed outlier: 4.005A  pdb=" N   THR E 189 " --> pdb=" O   ILE E 149 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ASP E 168 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'S' and resid 3 through 10
      removed outlier: 5.340A  pdb=" N   ILE S   4 " --> pdb=" O   VAL S 107 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   VAL S 107 " --> pdb=" O   ILE S   4 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   LYS S   6 " --> pdb=" O   VAL S 105 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   VAL S 105 " --> pdb=" O   LYS S   6 " (cutoff:3.500A)
      removed outlier: 5.440A  pdb=" N   ARG S   8 " --> pdb=" O   ILE S 103 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   ILE S 103 " --> pdb=" O   ARG S   8 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   SER S 108 " --> pdb=" O   VAL S  71 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   VAL S  71 " --> pdb=" O   SER S 108 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'U' and resid 33 through 35
      removed outlier: 7.123A  pdb=" N   ILE U  34 " --> pdb=" O   LYS U  25 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ASP U   8 " --> pdb=" O   VAL U  24 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'U' and resid 83 through 86
    Processing sheet with id=AA5, first strand: chain 'T' and resid 29 through 34
      removed outlier: 3.604A  pdb=" N   ALA T  83 " --> pdb=" O   LEU T  32 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL T  34 " --> pdb=" O   LYS T  81 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   LYS T  81 " --> pdb=" O   VAL T  34 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR T  86 " --> pdb=" O   VAL T  57 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   VAL T  57 " --> pdb=" O   THR T  86 " (cutoff:3.500A)

    181 hydrogen bonds defined for protein.
    534 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      506 hydrogen bonds
      816 hydrogen bond angles
      0 basepair planarities
      198 basepair parallelities
      310 stacking parallelities
  Total time for adding SS restraints: 8.47

  Time building geometry restraints manager: 5.02 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        1.92 -     2.52: 160
        2.52 -     3.11: 13075
        3.11 -     3.71: 33605
        3.71 -     4.30: 45916
        4.30 -     4.90: 62873
  Nonbonded interactions: 155629
  Sorted by model distance:
  nonbonded pdb=" O2'   A A 255 "
            pdb=" O4'   A A 256 "
     model   vdw
     1.924 3.040
  nonbonded pdb=" O2    C A  69 "
            pdb=" O2'   A A  73 "
     model   vdw
     1.948 3.040
  nonbonded pdb=" O2    C A 106 "
            pdb=" O2'   A A 294 "
     model   vdw
     1.965 3.040
  nonbonded pdb=" O2'   A A 126 "
            pdb=" O4'   A A 127 "
     model   vdw
     1.975 3.040
  nonbonded pdb=" O2'   A A 299 "
            pdb=" O4'   A A 300 "
     model   vdw
     1.988 3.040
  ... (remaining 155624 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.380
  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:          0.740
  Check model and map are aligned:         0.140
  Set scattering table:                    0.170
  Process input model:                     45.980
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.033  19762  Z= 0.073
  Angle     :  0.451  26.711  29894  Z= 0.212
  Chirality :  0.040   2.002   3913
  Planarity :  0.002   0.022   1349
  Dihedral  : 22.913 179.086  11622
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.39 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.39), residues: 507
  helix:  2.53 (0.37), residues: 213
  sheet:  0.56 (0.67), residues: 71
  loop :  0.03 (0.42), residues: 223

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

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

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

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.972 
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: 0.3571
  time to fit residues: 52.4729
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  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 87 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 29 optimal weight:    7.9990
   chunk 58 optimal weight:   20.0000
   chunk 46 optimal weight:    7.9990
   chunk 90 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 67 optimal weight:    4.9990
   chunk 104 optimal weight:    0.0030
   overall best weight:    4.7998

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

Flipped N/Q/H residues before XYZ refinement:
2  13 ASN
** E  24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  30 GLN
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 136 GLN
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U  65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T  15 HIS
T  48 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.052942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.038405 restraints weight = 203665.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.039476 restraints weight = 83447.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.040084 restraints weight = 53620.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.3929

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

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

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

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

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

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

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.894 
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: 0.8776 (t0) cc_final: 0.8092 (t0)
REVERT: E  163 ASN cc_start: 0.8537 (t0) cc_final: 0.8040 (m-40)
REVERT: E  188 MET cc_start: 0.9046 (ttt) cc_final: 0.8556 (tpt)
REVERT: E  199 MET cc_start: 0.9088 (mtm) cc_final: 0.8461 (ptp)
REVERT: S   68 ASP cc_start: 0.9516 (t0) cc_final: 0.9294 (t70)
REVERT: U   17 ASP cc_start: 0.7920 (t0) cc_final: 0.7628 (t0)
REVERT: T   11 LEU cc_start: 0.8717 (pt) cc_final: 0.8458 (pp)
REVERT: T   51 PHE cc_start: 0.8812 (m-80) cc_final: 0.8538 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 82
  average time/residue: 0.3154
  time to fit residues: 38.8507
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  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 99 optimal weight:    9.9990
   chunk 68 optimal weight:    9.9990
   chunk 81 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 88 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   chunk 113 optimal weight:    0.0670
   chunk 114 optimal weight:    6.9990
   chunk 87 optimal weight:    5.9990
   chunk 4 optimal weight:    7.9990
   overall best weight:    5.8126

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.049456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.035565 restraints weight = 208615.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.035994 restraints weight = 117440.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.036062 restraints weight = 76569.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.6394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  19762  Z= 0.315
  Angle     :  0.835  27.069  29894  Z= 0.403
  Chirality :  0.051   1.952   3913
  Planarity :  0.006   0.088   1349
  Dihedral  : 25.339 172.897  10573
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 30.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  4.29 %
    Favored  : 95.49 %
  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: -0.78 (0.35), residues: 507
  helix:  0.15 (0.33), residues: 218
  sheet: -1.13 (0.51), residues: 96
  loop : -0.75 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP T  80 
 HIS   0.007   0.002   HIS Y  41 
 PHE   0.023   0.003   PHE Y  26 
 TYR   0.020   0.003   TYR T  84 
 ARG   0.012   0.001   ARG E 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10247 (  687)
  hydrogen bonds       : angle       4.52879 ( 1350)
  covalent geometry    : bond        0.00584 (19762)
  covalent geometry    : angle       0.83462 (29894)

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

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.838 
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: 0.9264 (tm-30) cc_final: 0.9034 (tm-30)
REVERT: E  100 MET cc_start: 0.9485 (mtt) cc_final: 0.9056 (mtp)
REVERT: E  149 ILE cc_start: 0.9543 (tp) cc_final: 0.8387 (tp)
REVERT: E  195 GLN cc_start: 0.9661 (mt0) cc_final: 0.9348 (mt0)
REVERT: E  199 MET cc_start: 0.9278 (mtm) cc_final: 0.8433 (ptp)
REVERT: U    7 ASP cc_start: 0.9034 (m-30) cc_final: 0.8809 (m-30)
REVERT: T   31 VAL cc_start: 0.8821 (m) cc_final: 0.8523 (t)
REVERT: T   32 LEU cc_start: 0.8884 (mt) cc_final: 0.8509 (mp)
REVERT: T   87 LEU cc_start: 0.8356 (mt) cc_final: 0.8025 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 78
  average time/residue: 0.3389
  time to fit residues: 38.4002
Evaluate side-chains
  56 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 55
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 73 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   chunk 107 optimal weight:    8.9990
   chunk 39 optimal weight:    9.9990
   chunk 12 optimal weight:    9.9990
   chunk 27 optimal weight:    9.9990
   chunk 86 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   overall best weight:    2.3988

-------------------------------------------------------------------------------
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
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  68 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.051288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.037295 restraints weight = 203802.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.037998 restraints weight = 113669.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.038036 restraints weight = 69136.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.2811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.5979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  19762  Z= 0.155
  Angle     :  0.624  27.066  29894  Z= 0.299
  Chirality :  0.044   1.952   3913
  Planarity :  0.005   0.084   1349
  Dihedral  : 24.815 165.342  10573
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 16.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  4.29 %
    Favored  : 95.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.35), residues: 507
  helix:  0.64 (0.33), residues: 218
  sheet: -0.87 (0.51), residues: 95
  loop : -0.78 (0.42), residues: 194

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   0.019   0.002   PHE U  95 
 TYR   0.008   0.002   TYR S  38 
 ARG   0.008   0.001   ARG U  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06756 (  687)
  hydrogen bonds       : angle       3.91037 ( 1350)
  covalent geometry    : bond        0.00286 (19762)
  covalent geometry    : angle       0.62372 (29894)

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

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.967 
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: 0.8522 (ttt) cc_final: 0.8293 (ttt)
REVERT: E   25 GLU cc_start: 0.9237 (tm-30) cc_final: 0.9008 (tm-30)
REVERT: E  100 MET cc_start: 0.9403 (mtt) cc_final: 0.8873 (mtp)
REVERT: E  102 ARG cc_start: 0.9100 (mtm-85) cc_final: 0.8795 (ptp90)
REVERT: E  195 GLN cc_start: 0.9725 (mt0) cc_final: 0.9312 (mt0)
REVERT: E  199 MET cc_start: 0.9292 (mtm) cc_final: 0.8609 (mtp)
REVERT: S   68 ASP cc_start: 0.9587 (t0) cc_final: 0.9362 (t70)
REVERT: U    7 ASP cc_start: 0.8936 (m-30) cc_final: 0.8667 (m-30)
REVERT: T   31 VAL cc_start: 0.8553 (m) cc_final: 0.8177 (t)
REVERT: T   32 LEU cc_start: 0.8725 (mt) cc_final: 0.8358 (mp)
REVERT: T   51 PHE cc_start: 0.8655 (m-80) cc_final: 0.8376 (m-80)
REVERT: T   87 LEU cc_start: 0.8247 (mt) cc_final: 0.7972 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 82
  average time/residue: 0.3564
  time to fit residues: 43.4430
Evaluate side-chains
  61 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 6 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9980
   chunk 37 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 109 optimal weight:    6.9990
   chunk 60 optimal weight:   20.0000
   chunk 86 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 97 optimal weight:    4.9990
   chunk 26 optimal weight:   20.0000
   overall best weight:    4.7988

-------------------------------------------------------------------------------
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  52 ASN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  68 ASN
Y  15 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
T  15 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.049274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.034816 restraints weight = 208158.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.035769 restraints weight = 84913.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.036316 restraints weight = 55271.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.6925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  19762  Z= 0.273
  Angle     :  0.746  27.346  29894  Z= 0.359
  Chirality :  0.047   1.930   3913
  Planarity :  0.005   0.079   1349
  Dihedral  : 25.192 174.347  10573
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 27.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  3.84 %
    Favored  : 95.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.72 (0.35), residues: 507
  helix:  0.40 (0.33), residues: 219
  sheet: -1.26 (0.49), residues: 97
  loop : -0.90 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP T  80 
 HIS   0.004   0.001   HIS Y  41 
 PHE   0.015   0.002   PHE Y  26 
 TYR   0.016   0.002   TYR T  84 
 ARG   0.009   0.001   ARG U  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09386 (  687)
  hydrogen bonds       : angle       4.21573 ( 1350)
  covalent geometry    : bond        0.00499 (19762)
  covalent geometry    : angle       0.74585 (29894)

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

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   25 GLU cc_start: 0.9274 (tm-30) cc_final: 0.9059 (tm-30)
REVERT: E  199 MET cc_start: 0.9332 (mtm) cc_final: 0.8579 (mtp)
REVERT: U    7 ASP cc_start: 0.9043 (m-30) cc_final: 0.8830 (m-30)
REVERT: T   31 VAL cc_start: 0.8999 (m) cc_final: 0.8515 (t)
REVERT: T   32 LEU cc_start: 0.8560 (mt) cc_final: 0.8176 (mp)
  outliers start: 1
  outliers final: 1
  residues processed: 81
  average time/residue: 0.3470
  time to fit residues: 40.8821
Evaluate side-chains
  58 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 11 optimal weight:   10.0000
   chunk 98 optimal weight:    7.9990
   chunk 61 optimal weight:   20.0000
   chunk 42 optimal weight:   10.0000
   chunk 37 optimal weight:   20.0000
   chunk 28 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 69 optimal weight:    0.4980
   chunk 76 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   overall best weight:    6.2988

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

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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.048474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.034607 restraints weight = 217686.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.035589 restraints weight = 88019.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.036139 restraints weight = 56928.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.8414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  19762  Z= 0.344
  Angle     :  0.880  27.277  29894  Z= 0.425
  Chirality :  0.052   1.920   3913
  Planarity :  0.007   0.079   1349
  Dihedral  : 25.850 179.026  10573
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 35.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.69 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    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 (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: -1.55 (0.34), residues: 507
  helix: -0.26 (0.32), residues: 218
  sheet: -1.79 (0.48), residues: 97
  loop : -1.31 (0.41), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP T  80 
 HIS   0.006   0.002   HIS Y  41 
 PHE   0.021   0.003   PHE 2  18 
 TYR   0.016   0.002   TYR T  84 
 ARG   0.024   0.001   ARG E 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11748 (  687)
  hydrogen bonds       : angle       4.76699 ( 1350)
  covalent geometry    : bond        0.00638 (19762)
  covalent geometry    : angle       0.88013 (29894)

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

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.866 
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: 0.8434 (ttt) cc_final: 0.8187 (ttt)
REVERT: E   25 GLU cc_start: 0.9317 (tm-30) cc_final: 0.9058 (tm-30)
REVERT: E  117 ARG cc_start: 0.5778 (mtp180) cc_final: 0.5429 (mtp180)
REVERT: E  199 MET cc_start: 0.9386 (mtm) cc_final: 0.8765 (mtm)
REVERT: T   31 VAL cc_start: 0.8973 (m) cc_final: 0.8501 (t)
REVERT: T   32 LEU cc_start: 0.8584 (mt) cc_final: 0.8246 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.3519
  time to fit residues: 40.1005
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  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 88 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 48 optimal weight:    5.9990
   chunk 99 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 34 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   chunk 82 optimal weight:    7.9990
   chunk 101 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
E 115 GLN
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  31 GLN
** U  53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
U  68 ASN
** Y  41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.049858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.035988 restraints weight = 209878.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.036994 restraints weight = 80706.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.037589 restraints weight = 49831.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.8065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  19762  Z= 0.218
  Angle     :  0.696  27.130  29894  Z= 0.337
  Chirality :  0.046   1.941   3913
  Planarity :  0.005   0.041   1349
  Dihedral  : 25.455 174.102  10573
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 24.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  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 (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: -1.22 (0.34), residues: 507
  helix:  0.11 (0.32), residues: 219
  sheet: -1.41 (0.51), residues: 86
  loop : -1.44 (0.39), residues: 202

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   0.015   0.002   PHE Y  26 
 TYR   0.012   0.002   TYR T  84 
 ARG   0.007   0.001   ARG U  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08384 (  687)
  hydrogen bonds       : angle       4.22854 ( 1350)
  covalent geometry    : bond        0.00403 (19762)
  covalent geometry    : angle       0.69602 (29894)

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

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   22 MET cc_start: 0.8508 (ttt) cc_final: 0.8243 (ttt)
REVERT: E   30 GLN cc_start: 0.9521 (mt0) cc_final: 0.9276 (mt0)
REVERT: E   97 ASN cc_start: 0.8647 (t0) cc_final: 0.8400 (t0)
REVERT: E  102 ARG cc_start: 0.9202 (ptp-170) cc_final: 0.8847 (ptt-90)
REVERT: E  199 MET cc_start: 0.9328 (mtm) cc_final: 0.9007 (mtm)
REVERT: U    7 ASP cc_start: 0.9115 (m-30) cc_final: 0.8897 (m-30)
REVERT: Y    1 MET cc_start: 0.8916 (tpt) cc_final: 0.8710 (tpp)
REVERT: Y    4 LYS cc_start: 0.9497 (pptt) cc_final: 0.9157 (pptt)
REVERT: T   11 LEU cc_start: 0.8826 (pt) cc_final: 0.8593 (pp)
REVERT: T   31 VAL cc_start: 0.8870 (m) cc_final: 0.8540 (t)
REVERT: T   32 LEU cc_start: 0.8387 (mt) cc_final: 0.8072 (mt)
REVERT: T   87 LEU cc_start: 0.8806 (mt) cc_final: 0.8582 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 77
  average time/residue: 0.3518
  time to fit residues: 38.9552
Evaluate side-chains
  55 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 71 optimal weight:    0.4980
   chunk 48 optimal weight:    6.9990
   chunk 62 optimal weight:   30.0000
   chunk 6 optimal weight:    8.9990
   chunk 75 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   chunk 80 optimal weight:    0.9980
   chunk 99 optimal weight:   10.0000
   chunk 114 optimal weight:    8.9990
   overall best weight:    5.2986

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.048807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.034806 restraints weight = 213743.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.035829 restraints weight = 83353.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.036412 restraints weight = 52118.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.8707

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= 0.294
  Angle     :  0.793  27.239  29894  Z= 0.384
  Chirality :  0.049   1.923   3913
  Planarity :  0.005   0.043   1349
  Dihedral  : 25.762 179.429  10573
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 31.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.58 %
    Favored  : 98.19 %
  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: -1.49 (0.34), residues: 507
  helix: -0.09 (0.32), residues: 221
  sheet: -1.66 (0.49), residues: 87
  loop : -1.57 (0.40), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP T  80 
 HIS   0.004   0.001   HIS Y  41 
 PHE   0.017   0.002   PHE Y  26 
 TYR   0.013   0.002   TYR T  84 
 ARG   0.008   0.001   ARG U  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10401 (  687)
  hydrogen bonds       : angle       4.42582 ( 1350)
  covalent geometry    : bond        0.00544 (19762)
  covalent geometry    : angle       0.79337 (29894)

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

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   22 MET cc_start: 0.8498 (ttt) cc_final: 0.8204 (ttt)
REVERT: E  102 ARG cc_start: 0.9219 (ptp-170) cc_final: 0.8856 (ptt-90)
REVERT: E  199 MET cc_start: 0.9355 (mtm) cc_final: 0.8773 (mtm)
REVERT: Y    1 MET cc_start: 0.8811 (tpt) cc_final: 0.8586 (tpp)
REVERT: T   31 VAL cc_start: 0.8841 (m) cc_final: 0.8513 (t)
REVERT: T   32 LEU cc_start: 0.8415 (mt) cc_final: 0.8163 (mt)
  outliers start: 1
  outliers final: 1
  residues processed: 73
  average time/residue: 0.3649
  time to fit residues: 38.7696
Evaluate side-chains
  51 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 79 optimal weight:   10.0000
   chunk 93 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 95 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9980
   chunk 15 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 6 optimal weight:    7.9990
   chunk 69 optimal weight:    9.9990
   chunk 26 optimal weight:   20.0000
   overall best weight:    4.7988

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.048110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.033649 restraints weight = 203971.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.034682 restraints weight = 80737.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.035256 restraints weight = 51124.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.8847

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= 0.261
  Angle     :  0.742  27.136  29894  Z= 0.360
  Chirality :  0.048   1.930   3913
  Planarity :  0.005   0.044   1349
  Dihedral  : 25.681 175.878  10573
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 28.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.10 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.38 (0.34), residues: 507
  helix:  0.01 (0.32), residues: 221
  sheet: -1.65 (0.50), residues: 84
  loop : -1.50 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP T  80 
 HIS   0.004   0.001   HIS E 165 
 PHE   0.019   0.003   PHE E  23 
 TYR   0.013   0.002   TYR T  84 
 ARG   0.008   0.001   ARG U  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09225 (  687)
  hydrogen bonds       : angle       4.24744 ( 1350)
  covalent geometry    : bond        0.00482 (19762)
  covalent geometry    : angle       0.74240 (29894)

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

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.980 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 2   22 MET cc_start: 0.8623 (ttt) cc_final: 0.8362 (ttt)
REVERT: E  102 ARG cc_start: 0.9243 (ptp-170) cc_final: 0.8853 (ptt-90)
REVERT: E  184 ASP cc_start: 0.9121 (t0) cc_final: 0.8900 (t0)
REVERT: E  199 MET cc_start: 0.9322 (mtm) cc_final: 0.8667 (mtm)
REVERT: Y    4 LYS cc_start: 0.9524 (pptt) cc_final: 0.9298 (pptt)
REVERT: T   31 VAL cc_start: 0.8947 (m) cc_final: 0.8609 (t)
REVERT: T   32 LEU cc_start: 0.8373 (mt) cc_final: 0.8063 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.3486
  time to fit residues: 36.6298
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  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9990
   chunk 29 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 100 optimal weight:   10.0000
   chunk 18 optimal weight:   20.0000
   chunk 36 optimal weight:   20.0000
   chunk 6 optimal weight:    7.9990
   chunk 38 optimal weight:    9.9990
   chunk 98 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   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  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  60 HIS
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.047367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.032940 restraints weight = 210030.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.033871 restraints weight = 87676.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.034424 restraints weight = 57076.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.9302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040  19762  Z= 0.298
  Angle     :  0.798  27.329  29894  Z= 0.388
  Chirality :  0.050   1.922   3913
  Planarity :  0.005   0.044   1349
  Dihedral  : 25.875 179.744  10573
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 33.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  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: -1.61 (0.34), residues: 507
  helix: -0.18 (0.32), residues: 221
  sheet: -1.79 (0.49), residues: 84
  loop : -1.62 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP T  80 
 HIS   0.004   0.001   HIS Y  41 
 PHE   0.025   0.003   PHE E  23 
 TYR   0.011   0.002   TYR T  84 
 ARG   0.008   0.001   ARG U  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10520 (  687)
  hydrogen bonds       : angle       4.36708 ( 1350)
  covalent geometry    : bond        0.00551 (19762)
  covalent geometry    : angle       0.79751 (29894)

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

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

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

  1014 Ramachandran restraints generated.
    507 Oldfield, 0 Emsley, 507 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 443 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  102 ARG cc_start: 0.9246 (ptp-170) cc_final: 0.8862 (ptt-90)
REVERT: E  199 MET cc_start: 0.9348 (mtm) cc_final: 0.8704 (mtm)
REVERT: Y    4 LYS cc_start: 0.9449 (pptt) cc_final: 0.9196 (pptt)
REVERT: Y    7 ARG cc_start: 0.9268 (ptp-110) cc_final: 0.8737 (ttp80)
REVERT: T   31 VAL cc_start: 0.8931 (m) cc_final: 0.8603 (t)
REVERT: T   32 LEU cc_start: 0.8397 (mt) cc_final: 0.8123 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.3457
  time to fit residues: 37.2061
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  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 14 optimal weight:   20.0000
   chunk 49 optimal weight:    7.9990
   chunk 92 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 100 optimal weight:    4.9990
   chunk 60 optimal weight:   20.0000
   chunk 83 optimal weight:    1.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
2  16 HIS
** E  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  15 GLN
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 = 0.3165 r_free = 0.3165 target = 0.047346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.034033 restraints weight = 207835.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.034293 restraints weight = 128702.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.034321 restraints weight = 79981.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start:          0.9514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  19762  Z= 0.281
  Angle     :  0.768  27.250  29894  Z= 0.372
  Chirality :  0.049   1.926   3913
  Planarity :  0.005   0.045   1349
  Dihedral  : 25.868 177.257  10573
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 31.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.28 %
    Favored  : 91.72 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.00 %
    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 (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: -1.64 (0.34), residues: 507
  helix: -0.18 (0.32), residues: 221
  sheet: -1.84 (0.50), residues: 84
  loop : -1.66 (0.40), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP T  80 
 HIS   0.004   0.001   HIS Y  41 
 PHE   0.017   0.003   PHE Y  26 
 TYR   0.011   0.002   TYR T  84 
 ARG   0.008   0.001   ARG U  93 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09775 (  687)
  hydrogen bonds       : angle       4.27203 ( 1350)
  covalent geometry    : bond        0.00522 (19762)
  covalent geometry    : angle       0.76760 (29894)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4424.34 seconds
wall clock time: 79 minutes 34.05 seconds (4774.05 seconds total)