Starting phenix.real_space_refine
on Tue Jul 29 05:54:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nl0_12453/07_2025/7nl0_12453.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nl0_12453/07_2025/7nl0_12453.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7nl0_12453/07_2025/7nl0_12453.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nl0_12453/07_2025/7nl0_12453.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nl0_12453/07_2025/7nl0_12453.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nl0_12453/07_2025/7nl0_12453.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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     262      5.49       5
     S      14      5.16       5
     C    6334      2.51       5
     N    2121      2.21       5
     O    2632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11363
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 810
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "D"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 746
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 799
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 746
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 2715
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 2715
          Classifications: {'DNA': 131}
          Link IDs: {'rna3p': 130}
    Chain: "J"
      Number of atoms: 2656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 2656
          Classifications: {'DNA': 131}
          Link IDs: {'rna3p': 130}
  Time building chain proxies: 7.81, per 1000 atoms: 0.69
  Number of scatterers: 11363
  At special positions: 0
  Unit cell: (75.9676, 120.12, 116.873, 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      14     16.00
     P     262     15.00
     O    2632      8.00
     N    2121      7.00
     C    6334      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: 2.80
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 9 sheets defined
      73.0% alpha, 2.4% beta
      127 base pairs and 223 stacking pairs defined.
    Time for finding SS restraints: 5.73
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.820A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.671A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.802A  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: 4.505A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 53 through 81
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.591A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 121
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.500A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.787A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.638A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.727A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
      removed outlier: 3.513A  pdb=" N   LEU G 116 " --> pdb=" O   ALA G 113 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 120
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.350A  pdb=" N   ARG A  83 " --> 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 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.413A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (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 101 through 102
      removed outlier: 6.676A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.283A  pdb=" N   ARG E  83 " --> 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 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    409 hydrogen bonds defined for protein.
    1212 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      307 hydrogen bonds
      614 hydrogen bond angles
      0 basepair planarities
      127 basepair parallelities
      223 stacking parallelities
  Total time for adding SS restraints: 4.55

  Time building geometry restraints manager: 3.34 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2176
        1.33 -     1.45: 3809
        1.45 -     1.57: 5564
        1.57 -     1.69: 522
        1.69 -     1.81: 24
  Bond restraints: 12095
  Sorted by residual:
  bond pdb=" C3'  DA I  58 "
       pdb=" O3'  DA I  58 "
    ideal  model  delta    sigma   weight residual
    1.422  1.481 -0.059 3.00e-02 1.11e+03 3.88e+00
  bond pdb=" CG1 ILE H  86 "
       pdb=" CD1 ILE H  86 "
    ideal  model  delta    sigma   weight residual
    1.513  1.446  0.067 3.90e-02 6.57e+02 2.94e+00
  bond pdb=" C3'  DA I  14 "
       pdb=" O3'  DA I  14 "
    ideal  model  delta    sigma   weight residual
    1.422  1.472 -0.050 3.00e-02 1.11e+03 2.81e+00
  bond pdb=" CG1 ILE D  86 "
       pdb=" CD1 ILE D  86 "
    ideal  model  delta    sigma   weight residual
    1.513  1.452  0.061 3.90e-02 6.57e+02 2.49e+00
  bond pdb=" C3'  DC J -52 "
       pdb=" O3'  DC J -52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.462 -0.040 3.00e-02 1.11e+03 1.78e+00
  ... (remaining 12090 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 16646
        1.61 -     3.21: 753
        3.21 -     4.82: 36
        4.82 -     6.43: 15
        6.43 -     8.04: 1
  Bond angle restraints: 17451
  Sorted by residual:
  angle pdb=" N   VAL A 117 "
        pdb=" CA  VAL A 117 "
        pdb=" C   VAL A 117 "
      ideal   model   delta    sigma   weight residual
     113.71  107.75    5.96 9.50e-01 1.11e+00 3.94e+01
  angle pdb=" C   GLY G  37 "
        pdb=" N   ASN G  38 "
        pdb=" CA  ASN G  38 "
      ideal   model   delta    sigma   weight residual
     121.54  127.28   -5.74 1.91e+00 2.74e-01 9.04e+00
  angle pdb=" CA  VAL A 117 "
        pdb=" C   VAL A 117 "
        pdb=" N   THR A 118 "
      ideal   model   delta    sigma   weight residual
     119.87  116.36    3.51 1.34e+00 5.57e-01 6.87e+00
  angle pdb=" C3'  DA I  58 "
        pdb=" O3'  DA I  58 "
        pdb=" P    DT I  59 "
      ideal   model   delta    sigma   weight residual
     120.20  124.04   -3.84 1.50e+00 4.44e-01 6.54e+00
  angle pdb=" C3'  DA I  14 "
        pdb=" O3'  DA I  14 "
        pdb=" P    DA I  15 "
      ideal   model   delta    sigma   weight residual
     120.20  123.98   -3.78 1.50e+00 4.44e-01 6.34e+00
  ... (remaining 17446 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.14: 5243
       35.14 -    70.28: 1400
       70.28 -   105.43: 23
      105.43 -   140.57: 3
      140.57 -   175.71: 9
  Dihedral angle restraints: 6678
    sinusoidal: 4495
      harmonic: 2183
  Sorted by residual:
  dihedral pdb=" CA  TYR G  39 "
           pdb=" C   TYR G  39 "
           pdb=" N   SER G  40 "
           pdb=" CA  SER G  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.30   20.70     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" C4'  DG J  30 "
           pdb=" C3'  DG J  30 "
           pdb=" O3'  DG J  30 "
           pdb=" P    DA J  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   35.71 -175.71     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT I -17 "
           pdb=" C3'  DT I -17 "
           pdb=" O3'  DT I -17 "
           pdb=" P    DG I -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   33.83 -173.83     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 6675 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1249
       0.032 -    0.065: 536
       0.065 -    0.097: 147
       0.097 -    0.129: 47
       0.129 -    0.161: 4
  Chirality restraints: 1983
  Sorted by residual:
  chirality pdb=" CA  ASN G  38 "
            pdb=" N   ASN G  38 "
            pdb=" C   ASN G  38 "
            pdb=" CB  ASN G  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.50e-01
  chirality pdb=" P    DT I  59 "
            pdb=" OP1  DT I  59 "
            pdb=" OP2  DT I  59 "
            pdb=" O5'  DT I  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.48   -0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  VAL C 107 "
            pdb=" N   VAL C 107 "
            pdb=" C   VAL C 107 "
            pdb=" CB  VAL C 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.40e-01
  ... (remaining 1980 not shown)

  Planarity restraints: 1305
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -24 "   -0.027 2.00e-02 2.50e+03   1.18e-02 3.80e+00
        pdb=" N9   DA I -24 "    0.025 2.00e-02 2.50e+03
        pdb=" C8   DA I -24 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I -24 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DA I -24 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -24 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I -24 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I -24 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -24 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DA I -24 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I -24 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  16 "    0.027 2.00e-02 2.50e+03   1.10e-02 3.66e+00
        pdb=" N9   DG I  16 "   -0.018 2.00e-02 2.50e+03
        pdb=" C8   DG I  16 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I  16 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DG I  16 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6   DG I  16 "    0.006 2.00e-02 2.50e+03
        pdb=" O6   DG I  16 "    0.013 2.00e-02 2.50e+03
        pdb=" N1   DG I  16 "    0.004 2.00e-02 2.50e+03
        pdb=" C2   DG I  16 "   -0.004 2.00e-02 2.50e+03
        pdb=" N2   DG I  16 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I  16 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I  16 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  28 "    0.025 2.00e-02 2.50e+03   1.08e-02 3.50e+00
        pdb=" N9   DG I  28 "   -0.026 2.00e-02 2.50e+03
        pdb=" C8   DG I  28 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I  28 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DG I  28 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DG I  28 "    0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  28 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DG I  28 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DG I  28 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2   DG I  28 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DG I  28 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  28 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1302 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 559
        2.70 -     3.25: 9965
        3.25 -     3.80: 22342
        3.80 -     4.35: 27582
        4.35 -     4.90: 39438
  Nonbonded interactions: 99886
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D  65 "
            pdb=" OH  TYR F  98 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OD1 ASP C  90 "
            pdb=" N   GLU C  91 "
     model   vdw
     2.185 3.120
  nonbonded pdb=" NE  ARG A 131 "
            pdb=" OE2 GLU A 133 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.251 3.120
  ... (remaining 99881 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' and (resid 39 through 134 or (resid 135 and (name N or name CA or nam \ 
e C or name O or name CB ))))
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 24 through 102)
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 13 through 117)
}
ncs_group {
  reference = chain 'D'
  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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.310
  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:             0.020
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     33.760
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.020
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
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   0.067  12095  Z= 0.272
  Angle     :  0.709   8.036  17451  Z= 0.428
  Chirality :  0.039   0.161   1983
  Planarity :  0.004   0.040   1305
  Dihedral  : 29.742 175.712   5272
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.30), residues: 739
  helix:  1.29 (0.22), residues: 537
  sheet:  None (None), residues: 0
  loop : -1.90 (0.39), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS H  79 
 PHE   0.024   0.003   PHE C  25 
 TYR   0.012   0.002   TYR F  51 
 ARG   0.005   0.000   ARG G  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11327 (  716)
  hydrogen bonds       : angle       4.81605 ( 1826)
  covalent geometry    : bond        0.00625 (12095)
  covalent geometry    : angle       0.70914 (17451)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.828 
Fit side-chains
REVERT: E   59 GLU cc_start: 0.7178 (pp20) cc_final: 0.6897 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.3482
  time to fit residues: 59.2136
Evaluate side-chains
  121 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 29 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
D  92 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.141318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.102803 restraints weight = 18596.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.105332 restraints weight = 11818.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.106871 restraints weight = 9199.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.0668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12095  Z= 0.175
  Angle     :  0.646   8.570  17451  Z= 0.379
  Chirality :  0.037   0.153   1983
  Planarity :  0.004   0.037   1305
  Dihedral  : 32.882 175.280   3777
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  7.66 %
    Favored  : 91.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.31), residues: 739
  helix:  1.70 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.75 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.013   0.002   PHE C  25 
 TYR   0.016   0.002   TYR C  57 
 ARG   0.005   0.000   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05202 (  716)
  hydrogen bonds       : angle       3.43432 ( 1826)
  covalent geometry    : bond        0.00388 (12095)
  covalent geometry    : angle       0.64597 (17451)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 132
  time to evaluate  : 0.845 
Fit side-chains
REVERT: E   59 GLU cc_start: 0.7264 (pp20) cc_final: 0.7001 (pm20)
  outliers start: 8
  outliers final: 7
  residues processed: 134
  average time/residue: 0.3396
  time to fit residues: 58.5050
Evaluate side-chains
  130 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   36 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 52 optimal weight:   10.0000
   chunk 58 optimal weight:    0.6980
   chunk 79 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 53 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0570
   chunk 60 optimal weight:    4.9990
   chunk 84 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 48 optimal weight:    0.5980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.142451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.103771 restraints weight = 18622.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.106400 restraints weight = 11581.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.108043 restraints weight = 8929.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.0872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12095  Z= 0.162
  Angle     :  0.618   6.403  17451  Z= 0.365
  Chirality :  0.036   0.147   1983
  Planarity :  0.004   0.039   1305
  Dihedral  : 32.811 177.834   3777
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  9.41 %
    Favored  : 88.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.31), residues: 739
  helix:  2.06 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.64 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G  31 
 PHE   0.012   0.002   PHE A  67 
 TYR   0.011   0.001   TYR C  39 
 ARG   0.006   0.000   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04817 (  716)
  hydrogen bonds       : angle       3.24217 ( 1826)
  covalent geometry    : bond        0.00354 (12095)
  covalent geometry    : angle       0.61767 (17451)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.827 
Fit side-chains
REVERT: E   59 GLU cc_start: 0.7292 (pp20) cc_final: 0.7045 (pm20)
  outliers start: 12
  outliers final: 9
  residues processed: 136
  average time/residue: 0.3647
  time to fit residues: 65.8515
Evaluate side-chains
  135 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 126
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   36 ILE
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0670
   chunk 87 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 66 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.7322

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.142732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.104292 restraints weight = 18533.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.106768 restraints weight = 11770.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.108284 restraints weight = 9215.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12095  Z= 0.160
  Angle     :  0.606   8.831  17451  Z= 0.359
  Chirality :  0.036   0.146   1983
  Planarity :  0.004   0.039   1305
  Dihedral  : 32.762 178.728   3777
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.00 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.31), residues: 739
  helix:  2.18 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.64 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS G  31 
 PHE   0.022   0.002   PHE D  62 
 TYR   0.010   0.001   TYR C  39 
 ARG   0.002   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04437 (  716)
  hydrogen bonds       : angle       3.17692 ( 1826)
  covalent geometry    : bond        0.00356 (12095)
  covalent geometry    : angle       0.60566 (17451)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 132
  time to evaluate  : 0.864 
Fit side-chains
  outliers start: 13
  outliers final: 10
  residues processed: 137
  average time/residue: 0.3434
  time to fit residues: 61.5337
Evaluate side-chains
  133 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 75 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 69 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.142690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.104890 restraints weight = 18547.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.107110 restraints weight = 12447.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.108480 restraints weight = 10002.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069  12095  Z= 0.165
  Angle     :  0.596   5.704  17451  Z= 0.355
  Chirality :  0.035   0.144   1983
  Planarity :  0.004   0.041   1305
  Dihedral  : 32.703 179.563   3777
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 11.48 %
    Favored  : 86.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.31), residues: 739
  helix:  2.32 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.59 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G  31 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.009   0.001   TYR C  39 
 ARG   0.003   0.000   ARG G  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04325 (  716)
  hydrogen bonds       : angle       3.06316 ( 1826)
  covalent geometry    : bond        0.00377 (12095)
  covalent geometry    : angle       0.59620 (17451)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 0.847 
Fit side-chains
REVERT: H   69 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.8144 (mtm180)
  outliers start: 12
  outliers final: 11
  residues processed: 133
  average time/residue: 0.3097
  time to fit residues: 54.4915
Evaluate side-chains
  135 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 31 optimal weight:    0.0270
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 88 optimal weight:    6.9990
   chunk 5 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.143160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.104878 restraints weight = 18720.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.107391 restraints weight = 11859.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.108961 restraints weight = 9226.133|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12095  Z= 0.155
  Angle     :  0.595   8.676  17451  Z= 0.353
  Chirality :  0.035   0.141   1983
  Planarity :  0.004   0.040   1305
  Dihedral  : 32.676 179.618   3777
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 12.92 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.31), residues: 739
  helix:  2.42 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.49 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G  31 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.012   0.001   TYR C  57 
 ARG   0.004   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04151 (  716)
  hydrogen bonds       : angle       3.03903 ( 1826)
  covalent geometry    : bond        0.00347 (12095)
  covalent geometry    : angle       0.59492 (17451)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 0.881 
Fit side-chains
REVERT: H   69 ARG cc_start: 0.8465 (mtm-85) cc_final: 0.8198 (mtm180)
  outliers start: 12
  outliers final: 11
  residues processed: 132
  average time/residue: 0.3213
  time to fit residues: 55.8028
Evaluate side-chains
  135 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 124
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 92 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 27 optimal weight:    0.8980
   chunk 80 optimal weight:    6.9990
   chunk 87 optimal weight:    4.9990
   chunk 84 optimal weight:   10.0000
   chunk 0 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0570
   overall best weight:    0.9700

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.143094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.105201 restraints weight = 18824.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.107398 restraints weight = 12484.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.108763 restraints weight = 10058.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12095  Z= 0.165
  Angle     :  0.591   6.009  17451  Z= 0.351
  Chirality :  0.035   0.139   1983
  Planarity :  0.004   0.040   1305
  Dihedral  : 32.636 179.993   3777
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.24 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.31), residues: 739
  helix:  2.48 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.54 (0.40), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G  31 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.008   0.001   TYR C  50 
 ARG   0.002   0.000   ARG G  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04199 (  716)
  hydrogen bonds       : angle       2.99839 ( 1826)
  covalent geometry    : bond        0.00371 (12095)
  covalent geometry    : angle       0.59098 (17451)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.822 
Fit side-chains
REVERT: H   69 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8224 (mtm180)
REVERT: H   90 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7348 (mt-10)
  outliers start: 12
  outliers final: 11
  residues processed: 131
  average time/residue: 0.3085
  time to fit residues: 53.0257
Evaluate side-chains
  135 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 78 optimal weight:    7.9990
   chunk 19 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 71 optimal weight:   10.0000
   chunk 67 optimal weight:    0.9990
   chunk 80 optimal weight:    6.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.142249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.104233 restraints weight = 18834.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.106308 restraints weight = 12552.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.107681 restraints weight = 10193.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12095  Z= 0.185
  Angle     :  0.602   6.330  17451  Z= 0.355
  Chirality :  0.035   0.151   1983
  Planarity :  0.004   0.040   1305
  Dihedral  : 32.614 179.877   3777
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 12.76 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.30), residues: 739
  helix:  2.46 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.58 (0.40), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS G  31 
 PHE   0.012   0.002   PHE A  67 
 TYR   0.016   0.001   TYR C  57 
 ARG   0.003   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04381 (  716)
  hydrogen bonds       : angle       3.01633 ( 1826)
  covalent geometry    : bond        0.00423 (12095)
  covalent geometry    : angle       0.60160 (17451)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 1.003 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7690 (mtmm)
REVERT: H   69 ARG cc_start: 0.8487 (mtm-85) cc_final: 0.8250 (mtm180)
REVERT: H   90 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7373 (mt-10)
  outliers start: 15
  outliers final: 11
  residues processed: 134
  average time/residue: 0.3234
  time to fit residues: 57.3056
Evaluate side-chains
  136 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 77 optimal weight:    6.9990
   chunk 57 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
F  27 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.142801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.104024 restraints weight = 18636.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.106699 restraints weight = 11464.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.108340 restraints weight = 8814.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12095  Z= 0.157
  Angle     :  0.596   8.975  17451  Z= 0.352
  Chirality :  0.035   0.141   1983
  Planarity :  0.004   0.040   1305
  Dihedral  : 32.597 179.684   3777
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.56 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.31), residues: 739
  helix:  2.50 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.49 (0.41), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G  31 
 PHE   0.012   0.002   PHE A  67 
 TYR   0.018   0.001   TYR C  57 
 ARG   0.003   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04169 (  716)
  hydrogen bonds       : angle       2.99807 ( 1826)
  covalent geometry    : bond        0.00351 (12095)
  covalent geometry    : angle       0.59579 (17451)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.868 
Fit side-chains
REVERT: H   69 ARG cc_start: 0.8468 (mtm-85) cc_final: 0.8196 (mtm180)
REVERT: H   90 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7313 (mt-10)
  outliers start: 13
  outliers final: 12
  residues processed: 131
  average time/residue: 0.3423
  time to fit residues: 59.6621
Evaluate side-chains
  138 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 20 optimal weight:    0.0670
   chunk 89 optimal weight:    6.9990
   chunk 80 optimal weight:    6.9990
   chunk 70 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 90 optimal weight:    4.9990
   overall best weight:    1.1322

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.142781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.104803 restraints weight = 18678.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.106861 restraints weight = 12451.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.108243 restraints weight = 10108.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12095  Z= 0.174
  Angle     :  0.600   7.839  17451  Z= 0.354
  Chirality :  0.035   0.143   1983
  Planarity :  0.004   0.039   1305
  Dihedral  : 32.542 179.295   3777
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.72 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.32 (0.30), residues: 739
  helix:  2.50 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -1.43 (0.40), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS G  31 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.015   0.001   TYR C  57 
 ARG   0.003   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04221 (  716)
  hydrogen bonds       : angle       2.99650 ( 1826)
  covalent geometry    : bond        0.00396 (12095)
  covalent geometry    : angle       0.60000 (17451)

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

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

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1478 Ramachandran restraints generated.
    739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.939 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7684 (mtmm)
REVERT: H   69 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8226 (mtm180)
REVERT: H   90 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7320 (mt-10)
  outliers start: 13
  outliers final: 11
  residues processed: 133
  average time/residue: 0.3182
  time to fit residues: 55.7677
Evaluate side-chains
  141 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   90 MET
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue  115 VAL
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   90 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 27 optimal weight:    0.0870
   chunk 54 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 20 optimal weight:    0.4980
   chunk 78 optimal weight:    7.9990
   chunk 44 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 72 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9990
   chunk 73 optimal weight:    6.9990
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.143466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.105664 restraints weight = 18658.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.107813 restraints weight = 12441.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.109185 restraints weight = 10019.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12095  Z= 0.150
  Angle     :  0.590   7.652  17451  Z= 0.350
  Chirality :  0.035   0.140   1983
  Planarity :  0.004   0.041   1305
  Dihedral  : 32.538 179.122   3777
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.72 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.42 (0.31), residues: 739
  helix:  2.54 (0.21), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.32 (0.42), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  75 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.013   0.001   TYR C  57 
 ARG   0.003   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04077 (  716)
  hydrogen bonds       : angle       2.95748 ( 1826)
  covalent geometry    : bond        0.00332 (12095)
  covalent geometry    : angle       0.58995 (17451)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3273.21 seconds
wall clock time: 57 minutes 42.05 seconds (3462.05 seconds total)