Starting phenix.real_space_refine
on Fri Jul  3 01:32:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wlr_32591/07_2026/7wlr_32591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wlr_32591/07_2026/7wlr_32591.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wlr_32591/07_2026/7wlr_32591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wlr_32591/07_2026/7wlr_32591.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wlr_32591/07_2026/7wlr_32591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wlr_32591/07_2026/7wlr_32591.map"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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     289      5.49       5
     S       6      5.16       5
     C    6588      2.51       5
     N    2222      2.21       5
     O    2817      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11922
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 794
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 666
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 666
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 802
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 740
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 794
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 813
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 714
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.67, per 1000 atoms: 0.22
  Number of scatterers: 11922
  At special positions: 0
  Unit cell: (118.72, 86.92, 119.78, 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       6     16.00
     P     289     15.00
     O    2817      8.00
     N    2222      7.00
     C    6588      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: 0.82
  Conformation dependent library (CDL) restraints added in 231.9 milliseconds
  

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1420

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      74.5% alpha, 3.2% beta
      144 base pairs and 260 stacking pairs defined.
    Time for finding SS restraints: 1.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 58
    Processing helix  chain 'A' and resid 64 through 80
      removed outlier: 4.142A  pdb=" N   ASP A  78 " --> pdb=" O   GLU A  74 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   PHE A  79 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 115
      removed outlier: 3.688A  pdb=" N   ALA A 115 " --> pdb=" O   CYS A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 133
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.755A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.815A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.439A  pdb=" N   VAL C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 41 through 53
      removed outlier: 3.925A  pdb=" N   LYS D  47 " --> pdb=" O   SER D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 88
      removed outlier: 3.510A  pdb=" N   ASN D  88 " --> pdb=" O   LEU D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 94 through 106
    Processing helix  chain 'D' and resid 107 through 129
    Processing helix  chain 'E' and resid 45 through 58
    Processing helix  chain 'E' and resid 64 through 78
      removed outlier: 3.880A  pdb=" N   ASP E  78 " --> pdb=" O   GLU E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 115
      removed outlier: 3.642A  pdb=" N   ALA E 115 " --> pdb=" O   CYS E 111 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 132
      removed outlier: 3.507A  pdb=" N   ILE E 125 " --> pdb=" O   GLN E 121 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.999A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.426A  pdb=" N   VAL G  49 " --> pdb=" O   SER G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 41 through 53
    Processing helix  chain 'H' and resid 59 through 88
    Processing helix  chain 'H' and resid 94 through 106
    Processing helix  chain 'H' and resid 107 through 129
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85
      removed outlier: 7.306A  pdb=" N   ARG A  84 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.520A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.377A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  93 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85
      removed outlier: 7.067A  pdb=" N   ARG E  84 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.113A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  93 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    418 hydrogen bonds defined for protein.
    1233 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      367 hydrogen bonds
      730 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      260 stacking parallelities
  Total time for adding SS restraints: 1.70

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1476
        1.32 -     1.44: 4699
        1.44 -     1.56: 5959
        1.56 -     1.69: 577
        1.69 -     1.81: 10
  Bond restraints: 12721
  Sorted by residual:
  bond pdb=" N   ARG B  23 "
       pdb=" CA  ARG B  23 "
    ideal  model  delta    sigma   weight residual
    1.457  1.511 -0.054 1.29e-02 6.01e+03 1.75e+01
  bond pdb=" C6   DA I  97 "
       pdb=" N6   DA I  97 "
    ideal  model  delta    sigma   weight residual
    1.335  1.304  0.031 8.00e-03 1.56e+04 1.54e+01
  bond pdb=" C3'  DC I 122 "
       pdb=" C2'  DC I 122 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 8.00e-03 1.56e+04 1.46e+01
  bond pdb=" C3'  DC I  11 "
       pdb=" C2'  DC I  11 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.21e+01
  bond pdb=" C5'  DA I 123 "
       pdb=" C4'  DA I 123 "
    ideal  model  delta    sigma   weight residual
    1.512  1.536 -0.024 7.00e-03 2.04e+04 1.21e+01
  ... (remaining 12716 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 16282
        1.55 -     3.10: 1834
        3.10 -     4.65: 251
        4.65 -     6.20: 44
        6.20 -     7.74: 13
  Bond angle restraints: 18424
  Sorted by residual:
  angle pdb=" O5'  DA I 123 "
        pdb=" C5'  DA I 123 "
        pdb=" C4'  DA I 123 "
      ideal   model   delta    sigma   weight residual
     109.40  113.48   -4.08 8.00e-01 1.56e+00 2.60e+01
  angle pdb=" O4'  DA I 130 "
        pdb=" C1'  DA I 130 "
        pdb=" N9   DA I 130 "
      ideal   model   delta    sigma   weight residual
     108.00  104.63    3.37 7.00e-01 2.04e+00 2.31e+01
  angle pdb=" O4'  DA I  28 "
        pdb=" C4'  DA I  28 "
        pdb=" C3'  DA I  28 "
      ideal   model   delta    sigma   weight residual
     106.00  103.12    2.88 6.00e-01 2.78e+00 2.31e+01
  angle pdb=" N3   DT J  14 "
        pdb=" C4   DT J  14 "
        pdb=" O4   DT J  14 "
      ideal   model   delta    sigma   weight residual
     119.90  122.74   -2.84 6.00e-01 2.78e+00 2.24e+01
  angle pdb=" C   THR A  59 "
        pdb=" N   GLU A  60 "
        pdb=" CA  GLU A  60 "
      ideal   model   delta    sigma   weight residual
     120.82  127.74   -6.92 1.47e+00 4.63e-01 2.22e+01
  ... (remaining 18419 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.23: 4488
       21.23 -    42.46: 1286
       42.46 -    63.69: 1085
       63.69 -    84.92: 46
       84.92 -   106.15: 8
  Dihedral angle restraints: 6913
    sinusoidal: 4719
      harmonic: 2194
  Sorted by residual:
  dihedral pdb=" CA  GLY E  45 "
           pdb=" C   GLY E  45 "
           pdb=" N   THR E  46 "
           pdb=" CA  THR E  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.28  -25.72     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  GLY A  45 "
           pdb=" C   GLY A  45 "
           pdb=" N   THR A  46 "
           pdb=" CA  THR A  46 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.53  -25.47     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CA  ARG B  23 "
           pdb=" C   ARG B  23 "
           pdb=" N   ASP B  24 "
           pdb=" CA  ASP B  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.82  -23.18     0      5.00e+00 4.00e-02 2.15e+01
  ... (remaining 6910 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1727
       0.062 -    0.124: 339
       0.124 -    0.187: 27
       0.187 -    0.249: 10
       0.249 -    0.311: 4
  Chirality restraints: 2107
  Sorted by residual:
  chirality pdb=" CA  ARG F  23 "
            pdb=" N   ARG F  23 "
            pdb=" C   ARG F  23 "
            pdb=" CB  ARG F  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CA  LYS G 118 "
            pdb=" N   LYS G 118 "
            pdb=" C   LYS G 118 "
            pdb=" CB  LYS G 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" CA  THR A  46 "
            pdb=" N   THR A  46 "
            pdb=" C   THR A  46 "
            pdb=" CB  THR A  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.25    0.28 2.00e-01 2.50e+01 1.95e+00
  ... (remaining 2104 not shown)

  Planarity restraints: 1323
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  44 "    0.045 2.00e-02 2.50e+03   3.82e-02 2.92e+01
        pdb=" CG  TYR D  44 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  44 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  44 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  44 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  44 "   -0.049 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  44 "   -0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR D  44 "    0.068 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 101 "   -0.020 2.00e-02 2.50e+03   4.02e-02 1.62e+01
        pdb=" C   GLY B 101 "    0.070 2.00e-02 2.50e+03
        pdb=" O   GLY B 101 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   GLY B 102 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS H  53 "    0.014 2.00e-02 2.50e+03   3.24e-02 1.57e+01
        pdb=" CG  HIS H  53 "   -0.005 2.00e-02 2.50e+03
        pdb=" ND1 HIS H  53 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 HIS H  53 "   -0.040 2.00e-02 2.50e+03
        pdb=" CE1 HIS H  53 "   -0.035 2.00e-02 2.50e+03
        pdb=" NE2 HIS H  53 "    0.055 2.00e-02 2.50e+03
  ... (remaining 1320 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1741
        2.77 -     3.30: 10480
        3.30 -     3.83: 23372
        3.83 -     4.37: 27505
        4.37 -     4.90: 39362
  Nonbonded interactions: 102460
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  50 "
            pdb=" N2   DG J  96 "
     model   vdw
     2.232 2.496
  nonbonded pdb=" OH  TYR B  98 "
            pdb=" OD2 ASP H  72 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG  SER H  94 "
            pdb=" OE1 GLU H  97 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" OG  SER C  18 "
            pdb=" O   PHE C  25 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" OG  SER G  18 "
            pdb=" O   PHE G  25 "
     model   vdw
     2.383 3.040
  ... (remaining 102455 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 15 through 118)
}
ncs_group {
  reference = (chain 'D' and resid 38 through 129)
  selection = chain 'H'
}

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=0.00 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:             0.480
  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:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.160
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
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      :  0.007   0.060  12721  Z= 0.593
  Angle     :  1.005   7.744  18424  Z= 0.823
  Chirality :  0.052   0.311   2107
  Planarity :  0.010   0.124   1323
  Dihedral  : 29.271 106.152   5493
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.29), residues: 738
  helix:  1.78 (0.21), residues: 539
  sheet:  None (None), residues: 0
  loop : -0.77 (0.40), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  35 
 TYR   0.068   0.004   TYR D  44 
 PHE   0.008   0.001   PHE D  74 
 HIS   0.047   0.003   HIS H  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00722 /  0.59 (12721)
  covalent geometry    : angle       1.00535 /  0.82 (18424)
  hydrogen bonds       : bond        0.11505 /  7.63 (  785)
  hydrogen bonds       : angle       3.72291 /  2.73 ( 1963)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.289 
Fit side-chains
REVERT: B   91 LYS cc_start: 0.7799 (tttp) cc_final: 0.7208 (ttmm)
REVERT: C   41 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7398 (mt0)
REVERT: C   95 LYS cc_start: 0.7478 (ttmt) cc_final: 0.7248 (tttm)
REVERT: D   38 LYS cc_start: 0.7201 (tptm) cc_final: 0.6779 (tppt)
REVERT: D   89 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7467 (mttm)
REVERT: E  111 CYS cc_start: 0.6645 (p) cc_final: 0.6433 (p)
REVERT: G   36 ARG cc_start: 0.6975 (tpp80) cc_final: 0.6570 (mmt90)
REVERT: G  107 VAL cc_start: 0.8850 (p) cc_final: 0.8620 (m)
REVERT: H   75 GLU cc_start: 0.6979 (tp30) cc_final: 0.6624 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1442
  time to fit residues: 19.7525
Evaluate side-chains
  62 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN
D  51 GLN
D  53 HIS
D  88 ASN
E  77 GLN
E  94 GLN
F  25 ASN
G  73 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.167778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.115331 restraints weight = 14640.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.114041 restraints weight = 19750.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.114987 restraints weight = 19491.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.115088 restraints weight = 16317.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.115387 restraints weight = 17324.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12721  Z= 0.140
  Angle     :  0.622   6.009  18424  Z= 0.371
  Chirality :  0.044   0.217   2107
  Planarity :  0.005   0.057   1323
  Dihedral  : 31.967  99.367   4005
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  4.86 %
    Favored  : 94.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.47 (0.29), residues: 738
  helix:  2.35 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.53 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  96 
 TYR   0.010   0.001   TYR G  57 
 PHE   0.007   0.001   PHE H  74 
 HIS   0.007   0.001   HIS H  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00232 /  0.14 (12721)
  covalent geometry    : angle       0.62204 /  0.37 (18424)
  hydrogen bonds       : bond        0.05351 /  3.40 (  785)
  hydrogen bonds       : angle       2.91713 /  2.11 ( 1963)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7769 (tm-30)
REVERT: B   91 LYS cc_start: 0.8218 (tttp) cc_final: 0.7664 (ttmm)
REVERT: D   89 LYS cc_start: 0.8434 (mmmt) cc_final: 0.7771 (mttm)
REVERT: G   36 ARG cc_start: 0.6887 (tpp80) cc_final: 0.6614 (mmt90)
REVERT: G   73 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7755 (t0)
REVERT: G  107 VAL cc_start: 0.9055 (p) cc_final: 0.8757 (m)
  outliers start: 7
  outliers final: 2
  residues processed: 72
  average time/residue: 0.1229
  time to fit residues: 12.2694
Evaluate side-chains
  62 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   86 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 17 optimal weight:    9.9990
   chunk 98 optimal weight:   30.0000
   chunk 97 optimal weight:   30.0000
   chunk 78 optimal weight:   30.0000
   chunk 99 optimal weight:   40.0000
   chunk 7 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    2.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
D  51 GLN
D  53 HIS
F  25 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.161254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.108016 restraints weight = 14655.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.106665 restraints weight = 19670.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.107481 restraints weight = 18885.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.107634 restraints weight = 16459.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.107800 restraints weight = 17182.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  12721  Z= 0.197
  Angle     :  0.652   6.924  18424  Z= 0.378
  Chirality :  0.046   0.203   2107
  Planarity :  0.005   0.039   1323
  Dihedral  : 31.883 103.314   4005
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  8.93 %
    Favored  : 90.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.39 (0.30), residues: 738
  helix:  2.37 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.86 (0.40), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 129 
 TYR   0.016   0.002   TYR G  57 
 PHE   0.013   0.002   PHE G  25 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.20 (12721)
  covalent geometry    : angle       0.65183 /  0.38 (18424)
  hydrogen bonds       : bond        0.06032 /  3.90 (  785)
  hydrogen bonds       : angle       2.89362 /  2.09 ( 1963)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.8029 (tm-30) cc_final: 0.7722 (tm-30)
REVERT: B   91 LYS cc_start: 0.8432 (tttp) cc_final: 0.8000 (ttmm)
REVERT: D   46 TYR cc_start: 0.8315 (t80) cc_final: 0.7472 (t80)
REVERT: D   89 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7843 (mttm)
REVERT: G   36 ARG cc_start: 0.6890 (tpp80) cc_final: 0.6553 (mmt90)
  outliers start: 5
  outliers final: 4
  residues processed: 71
  average time/residue: 0.1199
  time to fit residues: 11.7211
Evaluate side-chains
  64 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain H residue   86 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 87 optimal weight:   40.0000
   chunk 84 optimal weight:   30.0000
   chunk 99 optimal weight:   50.0000
   chunk 85 optimal weight:   40.0000
   chunk 70 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 98 optimal weight:   30.0000
   chunk 53 optimal weight:   10.0000
   overall best weight:    2.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
D  51 GLN
E  77 GLN
F  25 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.160404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.107849 restraints weight = 14545.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.105967 restraints weight = 20291.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.106935 restraints weight = 20725.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.107304 restraints weight = 16775.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.107482 restraints weight = 17248.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12721  Z= 0.168
  Angle     :  0.614   6.012  18424  Z= 0.358
  Chirality :  0.044   0.209   2107
  Planarity :  0.004   0.036   1323
  Dihedral  : 31.661 109.197   4005
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.72 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.47 (0.30), residues: 738
  helix:  2.46 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.95 (0.39), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  67 
 TYR   0.013   0.002   TYR G  57 
 PHE   0.012   0.002   PHE G  25 
 HIS   0.005   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.17 (12721)
  covalent geometry    : angle       0.61405 /  0.36 (18424)
  hydrogen bonds       : bond        0.05490 /  3.49 (  785)
  hydrogen bonds       : angle       2.76406 /  2.00 ( 1963)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.297 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7678 (tm-30)
REVERT: B   91 LYS cc_start: 0.8414 (tttp) cc_final: 0.7981 (ttmm)
REVERT: D   46 TYR cc_start: 0.8326 (t80) cc_final: 0.7481 (t80)
REVERT: D   89 LYS cc_start: 0.8420 (mmmt) cc_final: 0.7840 (mttm)
REVERT: G   36 ARG cc_start: 0.6867 (tpp80) cc_final: 0.6520 (mmt90)
  outliers start: 11
  outliers final: 5
  residues processed: 84
  average time/residue: 0.1300
  time to fit residues: 14.8966
Evaluate side-chains
  69 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain H residue   86 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 24 optimal weight:    5.9990
   chunk 83 optimal weight:   20.0000
   chunk 90 optimal weight:   30.0000
   chunk 34 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
E  77 GLN
F  25 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.161312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.107318 restraints weight = 14827.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.106151 restraints weight = 19626.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.106868 restraints weight = 19004.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.107060 restraints weight = 16563.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.107190 restraints weight = 17876.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12721  Z= 0.146
  Angle     :  0.581   5.329  18424  Z= 0.345
  Chirality :  0.043   0.190   2107
  Planarity :  0.004   0.035   1323
  Dihedral  : 31.507 110.124   4005
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.66 %
    Favored  : 87.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.75 (0.30), residues: 738
  helix:  2.67 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -0.88 (0.39), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H 120 
 TYR   0.011   0.001   TYR G  57 
 PHE   0.006   0.001   PHE H  69 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.15 (12721)
  covalent geometry    : angle       0.58135 /  0.35 (18424)
  hydrogen bonds       : bond        0.05192 /  3.31 (  785)
  hydrogen bonds       : angle       2.72728 /  1.99 ( 1963)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7613 (tm-30)
REVERT: B   91 LYS cc_start: 0.8484 (tttp) cc_final: 0.8115 (ttmm)
REVERT: D   46 TYR cc_start: 0.8280 (t80) cc_final: 0.7483 (t80)
REVERT: D   89 LYS cc_start: 0.8376 (mmmt) cc_final: 0.7883 (mttm)
REVERT: G   36 ARG cc_start: 0.6913 (tpp80) cc_final: 0.6486 (mmt90)
REVERT: G   83 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8636 (mt)
REVERT: H   38 LYS cc_start: 0.7720 (tppt) cc_final: 0.7092 (mtpt)
  outliers start: 10
  outliers final: 6
  residues processed: 81
  average time/residue: 0.1139
  time to fit residues: 13.0625
Evaluate side-chains
  77 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain G residue   76 SER
Chi-restraints excluded: chain G residue   83 LEU
Chi-restraints excluded: chain H residue   86 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 82 optimal weight:   30.0000
   chunk 60 optimal weight:    0.0870
   chunk 24 optimal weight:    6.9990
   chunk 85 optimal weight:   40.0000
   chunk 36 optimal weight:   10.0000
   chunk 92 optimal weight:   20.0000
   chunk 74 optimal weight:   40.0000
   chunk 23 optimal weight:    0.9980
   chunk 87 optimal weight:   40.0000
   chunk 91 optimal weight:   20.0000
   overall best weight:    4.0166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
E  77 GLN
E  94 GLN
F  25 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.156749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.104262 restraints weight = 14765.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.102559 restraints weight = 22051.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.103549 restraints weight = 21586.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.103810 restraints weight = 17644.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.103901 restraints weight = 18862.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  12721  Z= 0.262
  Angle     :  0.704   8.622  18424  Z= 0.392
  Chirality :  0.048   0.206   2107
  Planarity :  0.005   0.039   1323
  Dihedral  : 31.749 113.122   4005
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 11.60 %
    Favored  : 86.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.07 (0.30), residues: 738
  helix:  2.22 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -1.31 (0.39), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  32 
 TYR   0.015   0.002   TYR G  57 
 PHE   0.014   0.002   PHE G  25 
 HIS   0.006   0.001   HIS H  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00615 /  0.26 (12721)
  covalent geometry    : angle       0.70373 /  0.39 (18424)
  hydrogen bonds       : bond        0.06556 /  4.22 (  785)
  hydrogen bonds       : angle       2.95617 /  2.17 ( 1963)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7962 (tm-30) cc_final: 0.7609 (tm-30)
REVERT: B   91 LYS cc_start: 0.8511 (tttp) cc_final: 0.8120 (ttmm)
REVERT: C   45 SER cc_start: 0.9005 (m) cc_final: 0.8799 (p)
REVERT: D   46 TYR cc_start: 0.8392 (t80) cc_final: 0.7593 (t80)
REVERT: D   89 LYS cc_start: 0.8430 (mmmt) cc_final: 0.7894 (mtmm)
REVERT: G   36 ARG cc_start: 0.7096 (tpp80) cc_final: 0.6552 (mmt90)
REVERT: G   83 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8780 (mt)
REVERT: H   38 LYS cc_start: 0.7779 (tppt) cc_final: 0.7156 (mtpt)
  outliers start: 13
  outliers final: 11
  residues processed: 81
  average time/residue: 0.1045
  time to fit residues: 11.9568
Evaluate side-chains
  78 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain G residue   83 LEU
Chi-restraints excluded: chain H residue   86 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 97 optimal weight:   30.0000
   chunk 82 optimal weight:   30.0000
   chunk 58 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0370
   chunk 81 optimal weight:   20.0000
   chunk 21 optimal weight:    0.9980
   chunk 89 optimal weight:   30.0000
   chunk 24 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  94 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
F  25 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.160856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.109081 restraints weight = 14570.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.107824 restraints weight = 21245.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.108627 restraints weight = 20322.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.108746 restraints weight = 17339.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.108958 restraints weight = 18520.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12721  Z= 0.125
  Angle     :  0.567   7.488  18424  Z= 0.340
  Chirality :  0.042   0.200   2107
  Planarity :  0.004   0.040   1323
  Dihedral  : 31.358 116.925   4005
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 13.17 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.81 (0.30), residues: 738
  helix:  2.78 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.05 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  84 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.006   0.001   PHE E  68 
 HIS   0.002   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00204 /  0.13 (12721)
  covalent geometry    : angle       0.56712 /  0.34 (18424)
  hydrogen bonds       : bond        0.04894 /  3.08 (  785)
  hydrogen bonds       : angle       2.67234 /  1.97 ( 1963)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7892 (tm-30) cc_final: 0.7601 (tm-30)
REVERT: B   91 LYS cc_start: 0.8460 (tttp) cc_final: 0.8054 (ttmm)
REVERT: D   46 TYR cc_start: 0.8153 (t80) cc_final: 0.7402 (t80)
REVERT: D   89 LYS cc_start: 0.8410 (mmmt) cc_final: 0.7830 (mttm)
REVERT: G   36 ARG cc_start: 0.7054 (tpp80) cc_final: 0.6616 (mmt90)
REVERT: H   38 LYS cc_start: 0.7743 (tppt) cc_final: 0.7201 (mtpt)
  outliers start: 5
  outliers final: 5
  residues processed: 76
  average time/residue: 0.1125
  time to fit residues: 12.1070
Evaluate side-chains
  72 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 91 optimal weight:   30.0000
   chunk 83 optimal weight:   30.0000
   chunk 35 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   chunk 2 optimal weight:    0.2980
   chunk 21 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   overall best weight:    1.7784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
E  77 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.159482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.108133 restraints weight = 14539.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.106208 restraints weight = 25071.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.107170 restraints weight = 22795.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.107446 restraints weight = 17877.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.107846 restraints weight = 17768.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  12721  Z= 0.151
  Angle     :  0.590   6.623  18424  Z= 0.346
  Chirality :  0.043   0.194   2107
  Planarity :  0.004   0.041   1323
  Dihedral  : 31.427 117.130   4005
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 13.17 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.80 (0.30), residues: 738
  helix:  2.78 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.08 (0.39), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 120 
 TYR   0.010   0.001   TYR G  57 
 PHE   0.009   0.001   PHE A  68 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00305 /  0.15 (12721)
  covalent geometry    : angle       0.58972 /  0.35 (18424)
  hydrogen bonds       : bond        0.05276 /  3.36 (  785)
  hydrogen bonds       : angle       2.72218 /  2.00 ( 1963)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.265 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7911 (tm-30) cc_final: 0.7554 (tm-30)
REVERT: B   91 LYS cc_start: 0.8461 (tttp) cc_final: 0.8055 (ttmm)
REVERT: D   46 TYR cc_start: 0.8289 (t80) cc_final: 0.7451 (t80)
REVERT: D   89 LYS cc_start: 0.8422 (mmmt) cc_final: 0.7908 (mttm)
REVERT: G   36 ARG cc_start: 0.7127 (tpp80) cc_final: 0.6642 (mmt90)
REVERT: G   83 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8708 (mt)
REVERT: H   38 LYS cc_start: 0.7763 (tppt) cc_final: 0.7250 (mtpt)
  outliers start: 6
  outliers final: 5
  residues processed: 71
  average time/residue: 0.1248
  time to fit residues: 12.2756
Evaluate side-chains
  70 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain G residue   83 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 96 optimal weight:   30.0000
   chunk 85 optimal weight:   40.0000
   chunk 80 optimal weight:   20.0000
   chunk 48 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 94 optimal weight:   20.0000
   chunk 4 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    2.1388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
E  77 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.159690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.106941 restraints weight = 14668.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.105145 restraints weight = 21637.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.106020 restraints weight = 21795.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.106257 restraints weight = 18127.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.106353 restraints weight = 16809.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12721  Z= 0.165
  Angle     :  0.592   6.419  18424  Z= 0.347
  Chirality :  0.043   0.194   2107
  Planarity :  0.004   0.042   1323
  Dihedral  : 31.425 118.189   4005
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.54 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.76 (0.30), residues: 738
  helix:  2.75 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.11 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  41 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.008   0.001   PHE H  69 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.17 (12721)
  covalent geometry    : angle       0.59195 /  0.35 (18424)
  hydrogen bonds       : bond        0.05289 /  3.36 (  785)
  hydrogen bonds       : angle       2.72876 /  2.01 ( 1963)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7574 (tm-30)
REVERT: B   91 LYS cc_start: 0.8525 (tttp) cc_final: 0.8158 (ttmm)
REVERT: D   46 TYR cc_start: 0.8256 (t80) cc_final: 0.7431 (t80)
REVERT: D   63 MET cc_start: 0.8818 (tpp) cc_final: 0.8558 (mmm)
REVERT: D   89 LYS cc_start: 0.8425 (mmmt) cc_final: 0.7930 (mttm)
REVERT: E   66 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8241 (mp)
REVERT: G   36 ARG cc_start: 0.7214 (tpp80) cc_final: 0.6733 (mmt90)
REVERT: G   83 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8718 (mt)
REVERT: H   38 LYS cc_start: 0.7774 (tppt) cc_final: 0.7179 (mtpt)
  outliers start: 12
  outliers final: 10
  residues processed: 75
  average time/residue: 0.1145
  time to fit residues: 12.1924
Evaluate side-chains
  75 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain G residue   83 LEU
Chi-restraints excluded: chain H residue   86 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 77 optimal weight:   30.0000
   chunk 39 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 63 optimal weight:    0.0670
   chunk 41 optimal weight:    0.6980
   chunk 86 optimal weight:   50.0000
   chunk 20 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7522

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
E  77 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.161654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.108830 restraints weight = 14564.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.106967 restraints weight = 21532.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.107952 restraints weight = 21367.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.108174 restraints weight = 17311.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.108284 restraints weight = 18214.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026  12721  Z= 0.120
  Angle     :  0.554   8.299  18424  Z= 0.333
  Chirality :  0.041   0.201   2107
  Planarity :  0.004   0.040   1323
  Dihedral  : 31.284 120.074   4005
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 13.01 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.12 (0.30), residues: 738
  helix:  3.02 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.97 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 120 
 TYR   0.008   0.001   TYR G  57 
 PHE   0.006   0.001   PHE E  68 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00194 /  0.12 (12721)
  covalent geometry    : angle       0.55378 /  0.33 (18424)
  hydrogen bonds       : bond        0.04719 /  2.96 (  785)
  hydrogen bonds       : angle       2.62850 /  1.94 ( 1963)

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

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

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1476 Ramachandran restraints generated.
    738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.202 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7569 (tm-30)
REVERT: B   91 LYS cc_start: 0.8495 (tttp) cc_final: 0.8106 (ttmm)
REVERT: D   46 TYR cc_start: 0.8126 (t80) cc_final: 0.7273 (t80)
REVERT: D   89 LYS cc_start: 0.8463 (mmmt) cc_final: 0.7904 (mttm)
REVERT: E   66 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8166 (mp)
REVERT: G   36 ARG cc_start: 0.7185 (tpp80) cc_final: 0.6727 (mmt90)
REVERT: G   83 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8647 (mt)
REVERT: H   38 LYS cc_start: 0.7905 (tppt) cc_final: 0.7329 (mtpt)
  outliers start: 9
  outliers final: 7
  residues processed: 75
  average time/residue: 0.1168
  time to fit residues: 12.4177
Evaluate side-chains
  73 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  111 CYS
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain E residue   97 VAL
Chi-restraints excluded: chain G residue   83 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 84 optimal weight:   30.0000
   chunk 65 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
E  77 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.161210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.108842 restraints weight = 14741.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.107002 restraints weight = 22208.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.107963 restraints weight = 22202.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.108209 restraints weight = 18119.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.108302 restraints weight = 17021.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  12721  Z= 0.136
  Angle     :  0.564   6.642  18424  Z= 0.336
  Chirality :  0.041   0.199   2107
  Planarity :  0.004   0.040   1323
  Dihedral  : 31.309 120.985   4005
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.32 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.06 (0.30), residues: 738
  helix:  2.97 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -0.98 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 120 
 TYR   0.009   0.001   TYR G  57 
 PHE   0.008   0.001   PHE A  68 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.14 (12721)
  covalent geometry    : angle       0.56354 /  0.34 (18424)
  hydrogen bonds       : bond        0.04968 /  3.13 (  785)
  hydrogen bonds       : angle       2.66331 /  1.96 ( 1963)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1411.85 seconds
wall clock time: 25 minutes 7.65 seconds (1507.65 seconds total)