Starting phenix.real_space_refine
on Wed Mar  4 06:07:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wlr_32591/03_2026/7wlr_32591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wlr_32591/03_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_32591/03_2026/7wlr_32591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wlr_32591/03_2026/7wlr_32591.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wlr_32591/03_2026/7wlr_32591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wlr_32591/03_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-5986/lib/python3.9/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: 3.07, per 1000 atoms: 0.26
  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: 0.94
  Conformation dependent library (CDL) restraints added in 427.6 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: 1.39
  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: 2.07

  Time building geometry restraints manager: 1.32 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=" C   ARG B  35 "
       pdb=" O   ARG B  35 "
    ideal  model  delta    sigma   weight residual
    1.237  1.197  0.040 1.19e-02 7.06e+03 1.14e+01
  bond pdb=" CZ  ARG C  32 "
       pdb=" NH2 ARG C  32 "
    ideal  model  delta    sigma   weight residual
    1.330  1.287  0.043 1.30e-02 5.92e+03 1.07e+01
  bond pdb=" CZ  ARG F  35 "
       pdb=" NH2 ARG F  35 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.02e+01
  bond pdb=" CZ  ARG A 135 "
       pdb=" NH2 ARG A 135 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.02e+01
  ... (remaining 12716 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 16892
        1.55 -     3.10: 1297
        3.10 -     4.65: 178
        4.65 -     6.20: 44
        6.20 -     7.74: 13
  Bond angle restraints: 18424
  Sorted by residual:
  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
  angle pdb=" C   SER G  14 "
        pdb=" N   THR G  15 "
        pdb=" CA  THR G  15 "
      ideal   model   delta    sigma   weight residual
     120.90  127.52   -6.62 1.41e+00 5.03e-01 2.21e+01
  angle pdb=" N   ARG F  23 "
        pdb=" CA  ARG F  23 "
        pdb=" C   ARG F  23 "
      ideal   model   delta    sigma   weight residual
     111.34  118.15   -6.81 1.49e+00 4.50e-01 2.09e+01
  angle pdb=" N   GLU G  91 "
        pdb=" CA  GLU G  91 "
        pdb=" C   GLU G  91 "
      ideal   model   delta    sigma   weight residual
     111.28  115.95   -4.67 1.09e+00 8.42e-01 1.84e+01
  angle pdb=" O   GLY D 108 "
        pdb=" C   GLY D 108 "
        pdb=" N   GLU D 109 "
      ideal   model   delta    sigma   weight residual
     122.13  118.01    4.12 9.90e-01 1.02e+00 1.74e+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: 1787
       0.062 -    0.124: 281
       0.124 -    0.187: 25
       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:             0.410
  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:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.740
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
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      :  0.006   0.060  12721  Z= 0.351
  Angle     :  0.884   7.744  18424  Z= 0.569
  Chirality :  0.049   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
  covalent geometry    : bond        0.00598 (12721)
  covalent geometry    : angle       0.88408 (18424)
  hydrogen bonds       : bond        0.11505 (  785)
  hydrogen bonds       : angle       3.72291 ( 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  : 0.178 
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: 0.1797
  time to fit residues: 24.1344
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  : 0.269 
-------------------------------------------------------------------------------
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:   10.0000
   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:    0.8980
   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...

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  53 HIS
D  88 ASN
E  77 GLN
E  94 GLN
F  25 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.167569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.115299 restraints weight = 14771.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.113318 restraints weight = 21267.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.114384 restraints weight = 20909.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.114647 restraints weight = 16573.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.114771 restraints weight = 18361.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12721  Z= 0.149
  Angle     :  0.542   6.622  18424  Z= 0.334
  Chirality :  0.033   0.132   2107
  Planarity :  0.004   0.042   1323
  Dihedral  : 31.226  92.924   4005
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  5.80 %
    Favored  : 93.73 %
  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:  2.83 (0.30), residues: 738
  helix:  2.62 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.45 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  78 
 TYR   0.010   0.001   TYR G  57 
 PHE   0.009   0.001   PHE H  74 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (12721)
  covalent geometry    : angle       0.54183 (18424)
  hydrogen bonds       : bond        0.04373 (  785)
  hydrogen bonds       : angle       2.72023 ( 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
  72 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7739 (tm-30)
REVERT: B   91 LYS cc_start: 0.8289 (tttp) cc_final: 0.7891 (ttmm)
REVERT: D   89 LYS cc_start: 0.8384 (mmmt) cc_final: 0.7822 (mttm)
REVERT: G   36 ARG cc_start: 0.6817 (tpp80) cc_final: 0.6586 (mmt90)
REVERT: G  107 VAL cc_start: 0.9124 (p) cc_final: 0.8780 (m)
  outliers start: 3
  outliers final: 1
  residues processed: 71
  average time/residue: 0.1309
  time to fit residues: 12.9212
Evaluate side-chains
  62 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   81 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 98 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 99 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
F  25 ASN
G  73 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.159577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.106230 restraints weight = 14859.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.104124 restraints weight = 24220.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.105050 restraints weight = 22982.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.105271 restraints weight = 19095.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.105673 restraints weight = 17731.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12721  Z= 0.215
  Angle     :  0.600   8.027  18424  Z= 0.358
  Chirality :  0.036   0.140   2107
  Planarity :  0.004   0.039   1323
  Dihedral  : 31.300  99.220   4005
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  8.46 %
    Favored  : 90.44 %
  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:  2.53 (0.30), residues: 738
  helix:  2.46 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.76 (0.39), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  96 
 TYR   0.013   0.002   TYR B  51 
 PHE   0.013   0.002   PHE G  25 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 (12721)
  covalent geometry    : angle       0.59959 (18424)
  hydrogen bonds       : bond        0.05589 (  785)
  hydrogen bonds       : angle       2.82181 ( 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
  89 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7946 (tm-30) cc_final: 0.7679 (tm-30)
REVERT: B   91 LYS cc_start: 0.8533 (tttp) cc_final: 0.8141 (ttmm)
REVERT: D   46 TYR cc_start: 0.8258 (t80) cc_final: 0.7498 (t80)
REVERT: D   63 MET cc_start: 0.9024 (tpp) cc_final: 0.8622 (tpp)
REVERT: D   89 LYS cc_start: 0.8328 (mmmt) cc_final: 0.7898 (mttm)
REVERT: G   36 ARG cc_start: 0.7025 (tpp80) cc_final: 0.6524 (mmt90)
REVERT: G   73 ASN cc_start: 0.8126 (OUTLIER) cc_final: 0.7751 (t0)
REVERT: H   38 LYS cc_start: 0.7770 (tppt) cc_final: 0.7126 (mtpt)
REVERT: H   75 GLU cc_start: 0.7716 (tp30) cc_final: 0.7397 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 84
  average time/residue: 0.1317
  time to fit residues: 15.2332
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  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  111 CYS
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   74 LYS
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:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 87 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 99 optimal weight:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 70 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 98 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   overall best weight:    2.5784

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
D  53 HIS
F  25 ASN
H  88 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.158671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.106041 restraints weight = 14641.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.104816 restraints weight = 21825.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.105659 restraints weight = 21236.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.105865 restraints weight = 17875.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.106066 restraints weight = 18734.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  12721  Z= 0.206
  Angle     :  0.580   6.443  18424  Z= 0.349
  Chirality :  0.035   0.138   2107
  Planarity :  0.004   0.037   1323
  Dihedral  : 30.989 100.049   4005
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 10.66 %
    Favored  : 88.24 %
  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:  2.46 (0.30), residues: 738
  helix:  2.50 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.07 (0.38), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  95 
 TYR   0.012   0.001   TYR B  51 
 PHE   0.010   0.002   PHE G  25 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 (12721)
  covalent geometry    : angle       0.58015 (18424)
  hydrogen bonds       : bond        0.05149 (  785)
  hydrogen bonds       : angle       2.78333 ( 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
  83 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7918 (tm-30) cc_final: 0.7607 (tm-30)
REVERT: B   91 LYS cc_start: 0.8526 (tttp) cc_final: 0.8135 (ttmm)
REVERT: D   46 TYR cc_start: 0.8289 (t80) cc_final: 0.7513 (t80)
REVERT: D   63 MET cc_start: 0.9026 (tpp) cc_final: 0.8610 (mmm)
REVERT: D   89 LYS cc_start: 0.8401 (mmmt) cc_final: 0.7899 (mttm)
REVERT: G   36 ARG cc_start: 0.7240 (tpp80) cc_final: 0.6767 (mmt90)
REVERT: H   38 LYS cc_start: 0.7746 (tppt) cc_final: 0.7237 (mtpt)
  outliers start: 7
  outliers final: 4
  residues processed: 79
  average time/residue: 0.1404
  time to fit residues: 15.1246
Evaluate side-chains
  77 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  107 VAL
Chi-restraints excluded: chain D residue  126 THR
Chi-restraints excluded: chain E residue   81 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 83 optimal weight:   10.0000
   chunk 90 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
A  94 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
D  53 HIS
G  73 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.160966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.105349 restraints weight = 14580.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.104062 restraints weight = 17581.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.104843 restraints weight = 16511.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.105096 restraints weight = 14445.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.105470 restraints weight = 14460.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12721  Z= 0.157
  Angle     :  0.534   7.093  18424  Z= 0.327
  Chirality :  0.033   0.133   2107
  Planarity :  0.004   0.037   1323
  Dihedral  : 30.798 100.497   4005
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 10.82 %
    Favored  : 88.24 %
  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:  2.92 (0.30), residues: 738
  helix:  2.81 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.85 (0.40), residues: 189

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   0.007   0.001   PHE A  68 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (12721)
  covalent geometry    : angle       0.53428 (18424)
  hydrogen bonds       : bond        0.04519 (  785)
  hydrogen bonds       : angle       2.62114 ( 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
  80 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7544 (tm-30)
REVERT: B   91 LYS cc_start: 0.8465 (tttp) cc_final: 0.8073 (ttmm)
REVERT: D   46 TYR cc_start: 0.8237 (t80) cc_final: 0.7430 (t80)
REVERT: D   63 MET cc_start: 0.8994 (tpp) cc_final: 0.8607 (tpp)
REVERT: D   89 LYS cc_start: 0.8440 (mmmt) cc_final: 0.7933 (mttm)
REVERT: G   36 ARG cc_start: 0.7233 (tpp80) cc_final: 0.6738 (mmt90)
REVERT: G   73 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7877 (t0)
REVERT: H   38 LYS cc_start: 0.7731 (tppt) cc_final: 0.7348 (mtpt)
  outliers start: 6
  outliers final: 4
  residues processed: 78
  average time/residue: 0.1337
  time to fit residues: 14.0450
Evaluate side-chains
  76 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain G residue   73 ASN
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:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 92 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   chunk 87 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   overall best weight:    3.5790

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
E  94 GLN
G  73 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.155941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.104477 restraints weight = 14621.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.102484 restraints weight = 24349.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.103477 restraints weight = 23393.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.103929 restraints weight = 17981.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.104386 restraints weight = 17429.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.3762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  12721  Z= 0.258
  Angle     :  0.630  10.237  18424  Z= 0.371
  Chirality :  0.038   0.150   2107
  Planarity :  0.005   0.041   1323
  Dihedral  : 31.234 103.608   4005
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 11.91 %
    Favored  : 86.21 %
  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:  2.29 (0.30), residues: 738
  helix:  2.37 (0.21), residues: 552
  sheet:  None (None), residues: 0
  loop : -1.21 (0.39), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  95 
 TYR   0.015   0.002   TYR B  51 
 PHE   0.010   0.002   PHE H  69 
 HIS   0.004   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00615 (12721)
  covalent geometry    : angle       0.63016 (18424)
  hydrogen bonds       : bond        0.06035 (  785)
  hydrogen bonds       : angle       2.91862 ( 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
  80 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 68
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7973 (tm-30) cc_final: 0.7639 (tm-30)
REVERT: B   91 LYS cc_start: 0.8547 (tttp) cc_final: 0.8109 (ttmm)
REVERT: D   46 TYR cc_start: 0.8342 (t80) cc_final: 0.7555 (t80)
REVERT: D   63 MET cc_start: 0.9018 (tpp) cc_final: 0.8803 (tpp)
REVERT: D   89 LYS cc_start: 0.8366 (mmmt) cc_final: 0.7956 (mttm)
REVERT: G   36 ARG cc_start: 0.7161 (tpp80) cc_final: 0.6708 (mmt90)
REVERT: G   73 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7843 (t0)
REVERT: H   38 LYS cc_start: 0.7892 (tppt) cc_final: 0.7495 (mtpt)
REVERT: H   75 GLU cc_start: 0.7808 (tp30) cc_final: 0.7555 (mt-10)
  outliers start: 12
  outliers final: 8
  residues processed: 77
  average time/residue: 0.1255
  time to fit residues: 13.2187
Evaluate side-chains
  77 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   71 ASN
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain H residue   86 SER
Chi-restraints excluded: chain H residue  126 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 34 optimal weight:    0.8980
   chunk 97 optimal weight:   10.0000
   chunk 82 optimal weight:   10.0000
   chunk 58 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 21 optimal weight:    0.6980
   chunk 89 optimal weight:   10.0000
   chunk 24 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  53 HIS
F  25 ASN
G  73 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 = 0.160843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.109177 restraints weight = 14574.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.107895 restraints weight = 20372.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.108699 restraints weight = 20054.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.108885 restraints weight = 17389.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.108976 restraints weight = 16445.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12721  Z= 0.149
  Angle     :  0.530   7.723  18424  Z= 0.325
  Chirality :  0.033   0.133   2107
  Planarity :  0.004   0.042   1323
  Dihedral  : 30.727 101.507   4005
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.91 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.92 (0.30), residues: 738
  helix:  2.89 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.11 (0.39), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 120 
 TYR   0.010   0.001   TYR G  57 
 PHE   0.008   0.001   PHE A  68 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (12721)
  covalent geometry    : angle       0.52960 (18424)
  hydrogen bonds       : bond        0.04349 (  785)
  hydrogen bonds       : angle       2.60830 ( 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
  84 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7585 (tm-30)
REVERT: B   91 LYS cc_start: 0.8500 (tttp) cc_final: 0.8106 (ttmm)
REVERT: D   46 TYR cc_start: 0.8239 (t80) cc_final: 0.7371 (t80)
REVERT: D   63 MET cc_start: 0.8945 (tpp) cc_final: 0.8675 (tpp)
REVERT: D   89 LYS cc_start: 0.8421 (mmmt) cc_final: 0.7982 (mttm)
REVERT: E   66 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8249 (mp)
REVERT: G   36 ARG cc_start: 0.7200 (tpp80) cc_final: 0.6757 (mmt90)
REVERT: G   73 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7829 (t0)
REVERT: G   83 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8690 (mt)
REVERT: H   38 LYS cc_start: 0.8016 (tppt) cc_final: 0.7603 (mtpt)
  outliers start: 9
  outliers final: 5
  residues processed: 82
  average time/residue: 0.1332
  time to fit residues: 14.8522
Evaluate side-chains
  82 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
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 E residue   66 LEU
Chi-restraints excluded: chain G residue   73 ASN
Chi-restraints excluded: chain G residue   83 LEU
Chi-restraints excluded: chain H residue   86 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 91 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0470
   chunk 21 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0170
   chunk 32 optimal weight:    6.9990
   overall best weight:    0.7918

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  53 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.161183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.108583 restraints weight = 14540.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.107306 restraints weight = 20561.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.108151 restraints weight = 20636.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.108243 restraints weight = 17386.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.108414 restraints weight = 18874.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12721  Z= 0.143
  Angle     :  0.519   6.649  18424  Z= 0.319
  Chirality :  0.032   0.131   2107
  Planarity :  0.004   0.040   1323
  Dihedral  : 30.716 100.285   4005
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 11.44 %
    Favored  : 87.46 %
  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:  3.17 (0.30), residues: 738
  helix:  3.08 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -1.02 (0.39), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  77 
 TYR   0.008   0.001   TYR G  57 
 PHE   0.007   0.001   PHE A  68 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (12721)
  covalent geometry    : angle       0.51938 (18424)
  hydrogen bonds       : bond        0.04225 (  785)
  hydrogen bonds       : angle       2.56727 ( 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
  81 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7578 (tm-30)
REVERT: B   91 LYS cc_start: 0.8509 (tttp) cc_final: 0.8130 (ttmm)
REVERT: D   46 TYR cc_start: 0.8266 (t80) cc_final: 0.7341 (t80)
REVERT: D   63 MET cc_start: 0.8929 (tpp) cc_final: 0.8692 (tpp)
REVERT: D   89 LYS cc_start: 0.8441 (mmmt) cc_final: 0.7945 (mttm)
REVERT: E   66 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8246 (mp)
REVERT: G   36 ARG cc_start: 0.7189 (tpp80) cc_final: 0.6750 (mmt90)
REVERT: G   83 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8685 (mt)
REVERT: H   38 LYS cc_start: 0.8021 (tppt) cc_final: 0.7608 (mtpt)
  outliers start: 7
  outliers final: 5
  residues processed: 80
  average time/residue: 0.1247
  time to fit residues: 13.6478
Evaluate side-chains
  79 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
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  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue   66 LEU
Chi-restraints excluded: chain G residue   83 LEU
Chi-restraints excluded: chain H residue   86 SER
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:   10.0000
   chunk 85 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 48 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 94 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0670
   chunk 29 optimal weight:    4.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    2.7524

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
D  53 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.157941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.102382 restraints weight = 14582.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.100977 restraints weight = 18393.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.101792 restraints weight = 17385.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.101981 restraints weight = 15162.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.102354 restraints weight = 15306.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  12721  Z= 0.215
  Angle     :  0.578   7.886  18424  Z= 0.345
  Chirality :  0.035   0.140   2107
  Planarity :  0.004   0.042   1323
  Dihedral  : 30.988 103.166   4005
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.13 %
    Favored  : 87.15 %
  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:  2.73 (0.30), residues: 738
  helix:  2.74 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop : -1.16 (0.39), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  77 
 TYR   0.011   0.001   TYR B  51 
 PHE   0.008   0.001   PHE H  69 
 HIS   0.004   0.001   HIS H  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 (12721)
  covalent geometry    : angle       0.57754 (18424)
  hydrogen bonds       : bond        0.05393 (  785)
  hydrogen bonds       : angle       2.76574 ( 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: 11
    poor density    : 66
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A   42 TYR cc_start: 0.7973 (m-80) cc_final: 0.7563 (m-10)
REVERT: A   77 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7604 (tm-30)
REVERT: B   91 LYS cc_start: 0.8647 (tttp) cc_final: 0.8208 (ttmm)
REVERT: D   46 TYR cc_start: 0.8315 (t80) cc_final: 0.7429 (t80)
REVERT: D   63 MET cc_start: 0.8997 (tpp) cc_final: 0.8739 (tpp)
REVERT: D   89 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8006 (mttm)
REVERT: E   66 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8405 (mm)
REVERT: G   36 ARG cc_start: 0.7201 (tpp80) cc_final: 0.6784 (mmt90)
REVERT: G   83 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8712 (mt)
REVERT: H   38 LYS cc_start: 0.7996 (tppt) cc_final: 0.7551 (mtpt)
  outliers start: 11
  outliers final: 8
  residues processed: 75
  average time/residue: 0.1186
  time to fit residues: 12.5804
Evaluate side-chains
  74 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
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  118 VAL
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 E residue   66 LEU
Chi-restraints excluded: chain G residue   83 LEU
Chi-restraints excluded: chain H residue   86 SER
Chi-restraints excluded: chain H residue  126 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 53 optimal weight:   20.0000
   chunk 63 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 86 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.160212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.108123 restraints weight = 14485.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.106739 restraints weight = 20118.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.107559 restraints weight = 20231.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.107743 restraints weight = 16954.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.107956 restraints weight = 17778.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.4072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12721  Z= 0.152
  Angle     :  0.528   8.741  18424  Z= 0.322
  Chirality :  0.033   0.136   2107
  Planarity :  0.004   0.041   1323
  Dihedral  : 30.710 100.132   4005
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 11.60 %
    Favored  : 87.30 %
  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:  3.05 (0.30), residues: 738
  helix:  2.97 (0.21), residues: 550
  sheet:  None (None), residues: 0
  loop : -1.08 (0.40), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  77 
 TYR   0.009   0.001   TYR G  57 
 PHE   0.008   0.001   PHE A  68 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (12721)
  covalent geometry    : angle       0.52845 (18424)
  hydrogen bonds       : bond        0.04464 (  785)
  hydrogen bonds       : angle       2.60041 ( 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: 7
    poor density    : 69
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   77 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7593 (tm-30)
REVERT: B   91 LYS cc_start: 0.8519 (tttp) cc_final: 0.8124 (ttmm)
REVERT: D   46 TYR cc_start: 0.8296 (t80) cc_final: 0.7361 (t80)
REVERT: D   63 MET cc_start: 0.8937 (tpp) cc_final: 0.8704 (tpp)
REVERT: D   89 LYS cc_start: 0.8397 (mmmt) cc_final: 0.7967 (mttm)
REVERT: E   66 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8265 (mp)
REVERT: G   36 ARG cc_start: 0.7126 (tpp80) cc_final: 0.6737 (mmt90)
REVERT: G   83 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8736 (mt)
REVERT: H   38 LYS cc_start: 0.8016 (tppt) cc_final: 0.7634 (mtpt)
  outliers start: 7
  outliers final: 5
  residues processed: 75
  average time/residue: 0.1290
  time to fit residues: 13.2269
Evaluate side-chains
  75 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
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  125 ILE
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue   66 LEU
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 94 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 84 optimal weight:    9.9990
   chunk 65 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.160642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.108864 restraints weight = 14665.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.107198 restraints weight = 21243.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.108137 restraints weight = 21686.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.108530 restraints weight = 17274.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.108669 restraints weight = 17456.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.4087

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= 0.150
  Angle     :  0.526   7.970  18424  Z= 0.321
  Chirality :  0.033   0.135   2107
  Planarity :  0.004   0.039   1323
  Dihedral  : 30.712 100.167   4005
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 6.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.97 %
    Favored  : 87.46 %
  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:  3.10 (0.30), residues: 738
  helix:  3.02 (0.21), residues: 549
  sheet:  None (None), residues: 0
  loop : -1.07 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  77 
 TYR   0.008   0.001   TYR G  57 
 PHE   0.007   0.001   PHE E  68 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (12721)
  covalent geometry    : angle       0.52605 (18424)
  hydrogen bonds       : bond        0.04423 (  785)
  hydrogen bonds       : angle       2.59592 ( 1963)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1437.01 seconds
wall clock time: 25 minutes 30.45 seconds (1530.45 seconds total)