Starting phenix.real_space_refine
on Mon Jul 28 10:11:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dbh_30631/07_2025/7dbh_30631.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dbh_30631/07_2025/7dbh_30631.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dbh_30631/07_2025/7dbh_30631.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dbh_30631/07_2025/7dbh_30631.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dbh_30631/07_2025/7dbh_30631.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dbh_30631/07_2025/7dbh_30631.cif"
  }
  resolution = 3.6
  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=   0.001 sd=   0.004
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     250      5.49       5
     S      14      5.16       5
     C    5902      2.51       5
     N    1973      2.21       5
     O    2492      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 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: 10631
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 612
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 2, 'TRANS': 75}
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 726
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 4, 'TRANS': 89}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "D"
      Number of atoms: 721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 721
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 677
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 677
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 2, 'TRANS': 82}
    Chain: "F"
      Number of atoms: 614
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 614
          Classifications: {'peptide': 77}
          Link IDs: {'PTRANS': 1, 'TRANS': 75}
    Chain: "G"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 740
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "H"
      Number of atoms: 724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 724
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "I"
      Number of atoms: 2563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 2563
          Classifications: {'DNA': 126}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 125}
    Chain: "J"
      Number of atoms: 2597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 2597
          Classifications: {'DNA': 126}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 125}
  Time building chain proxies: 6.14, per 1000 atoms: 0.58
  Number of scatterers: 10631
  At special positions: 0
  Unit cell: (122.1, 75.9, 115.5, 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     250     15.00
     O    2492      8.00
     N    1973      7.00
     C    5902      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: 3.09
  Conformation dependent library (CDL) restraints added in 717.8 milliseconds
  

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1296

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 10 sheets defined
      76.8% alpha, 2.9% beta
      116 base pairs and 191 stacking pairs defined.
    Time for finding SS restraints: 5.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.717A  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 131
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.608A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'C' and resid 18 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.314A  pdb=" N   VAL C  49 " --> pdb=" O   ALA 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 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 124
    Processing helix  chain 'E' and resid 49 through 57
      removed outlier: 3.638A  pdb=" N   SER E  57 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
    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 47 through 76
      removed outlier: 4.151A  pdb=" N   TYR F  51 " --> pdb=" O   SER F  47 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   GLU F  52 " --> pdb=" O   GLY F  48 " (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: 4.383A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 98
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
      removed outlier: 3.824A  pdb=" N   SER H 124 " --> pdb=" O   LYS H 120 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.777A  pdb=" N   CYS 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: 7.821A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (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: 6.864A  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: 6.435A  pdb=" N   CYS 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 42 through 43
      removed outlier: 7.257A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (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

    403 hydrogen bonds defined for protein.
    1188 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      303 hydrogen bonds
      594 hydrogen bond angles
      0 basepair planarities
      116 basepair parallelities
      191 stacking parallelities
  Total time for adding SS restraints: 4.04

  Time building geometry restraints manager: 3.60 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: 2284
        1.33 -     1.45: 3447
        1.45 -     1.57: 5077
        1.57 -     1.69: 500
        1.69 -     1.81: 22
  Bond restraints: 11330
  Sorted by residual:
  bond pdb=" N   ILE E 130 "
       pdb=" CA  ILE E 130 "
    ideal  model  delta    sigma   weight residual
    1.462  1.495 -0.033 1.14e-02 7.69e+03 8.54e+00
  bond pdb=" N   ARG A  63 "
       pdb=" CA  ARG A  63 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.23e-02 6.61e+03 7.54e+00
  bond pdb=" N   ARG G  42 "
       pdb=" CA  ARG G  42 "
    ideal  model  delta    sigma   weight residual
    1.454  1.484 -0.031 1.23e-02 6.61e+03 6.18e+00
  bond pdb=" N   GLY H  32 "
       pdb=" CA  GLY H  32 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.17e+00
  bond pdb=" N   CYS E 131 "
       pdb=" CA  CYS E 131 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.03e+00
  ... (remaining 11325 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 14978
        1.25 -     2.50: 1181
        2.50 -     3.75: 211
        3.75 -     5.00: 11
        5.00 -     6.25: 4
  Bond angle restraints: 16385
  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  109.21    4.50 9.50e-01 1.11e+00 2.25e+01
  angle pdb=" O   CYS E 131 "
        pdb=" C   CYS E 131 "
        pdb=" N   ARG E 132 "
      ideal   model   delta    sigma   weight residual
     122.12  125.71   -3.59 1.06e+00 8.90e-01 1.15e+01
  angle pdb=" C   ARG A 132 "
        pdb=" CA  ARG A 132 "
        pdb=" CB  ARG A 132 "
      ideal   model   delta    sigma   weight residual
     110.10  116.35   -6.25 1.90e+00 2.77e-01 1.08e+01
  angle pdb=" N   ARG C  17 "
        pdb=" CA  ARG C  17 "
        pdb=" C   ARG C  17 "
      ideal   model   delta    sigma   weight residual
     113.43  109.44    3.99 1.26e+00 6.30e-01 1.00e+01
  angle pdb=" N   ARG B  55 "
        pdb=" CA  ARG B  55 "
        pdb=" C   ARG B  55 "
      ideal   model   delta    sigma   weight residual
     111.28  107.92    3.36 1.09e+00 8.42e-01 9.51e+00
  ... (remaining 16380 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.66: 4874
       33.66 -    67.32: 1205
       67.32 -   100.98: 41
      100.98 -   134.65: 5
      134.65 -   168.31: 5
  Dihedral angle restraints: 6130
    sinusoidal: 4116
      harmonic: 2014
  Sorted by residual:
  dihedral pdb=" C   ARG A 132 "
           pdb=" N   ARG A 132 "
           pdb=" CA  ARG A 132 "
           pdb=" CB  ARG A 132 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.04   10.44     0      2.50e+00 1.60e-01 1.74e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   51.69  168.31     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" C4'  DC J -58 "
           pdb=" C3'  DC J -58 "
           pdb=" O3'  DC J -58 "
           pdb=" P    DT J -57 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   51.95  168.05     1      3.50e+01 8.16e-04 1.55e+01
  ... (remaining 6127 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1510
       0.060 -    0.120: 349
       0.120 -    0.180: 14
       0.180 -    0.241: 0
       0.241 -    0.301: 1
  Chirality restraints: 1874
  Sorted by residual:
  chirality pdb=" CA  ARG A 132 "
            pdb=" N   ARG A 132 "
            pdb=" C   ARG A 132 "
            pdb=" CB  ARG A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CA  LEU E 100 "
            pdb=" N   LEU E 100 "
            pdb=" C   LEU E 100 "
            pdb=" CB  LEU E 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.17 2.00e-01 2.50e+01 7.63e-01
  chirality pdb=" CA  LEU F  37 "
            pdb=" N   LEU F  37 "
            pdb=" C   LEU F  37 "
            pdb=" CB  LEU F  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.91e-01
  ... (remaining 1871 not shown)

  Planarity restraints: 1197
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J -36 "    0.016 2.00e-02 2.50e+03   1.08e-02 3.50e+00
        pdb=" N9   DG J -36 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8   DG J -36 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DG J -36 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG J -36 "    0.000 2.00e-02 2.50e+03
        pdb=" C6   DG J -36 "   -0.021 2.00e-02 2.50e+03
        pdb=" O6   DG J -36 "    0.015 2.00e-02 2.50e+03
        pdb=" N1   DG J -36 "    0.004 2.00e-02 2.50e+03
        pdb=" C2   DG J -36 "    0.008 2.00e-02 2.50e+03
        pdb=" N2   DG J -36 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DG J -36 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DG J -36 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  35 "   -0.007 2.00e-02 2.50e+03   1.20e-02 3.22e+00
        pdb=" N1   DC I  35 "    0.004 2.00e-02 2.50e+03
        pdb=" C2   DC I  35 "   -0.007 2.00e-02 2.50e+03
        pdb=" O2   DC I  35 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DC I  35 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4   DC I  35 "    0.028 2.00e-02 2.50e+03
        pdb=" N4   DC I  35 "   -0.017 2.00e-02 2.50e+03
        pdb=" C5   DC I  35 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DC I  35 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I   6 "   -0.022 2.00e-02 2.50e+03   1.16e-02 3.05e+00
        pdb=" N1   DC I   6 "    0.023 2.00e-02 2.50e+03
        pdb=" C2   DC I   6 "   -0.006 2.00e-02 2.50e+03
        pdb=" O2   DC I   6 "    0.009 2.00e-02 2.50e+03
        pdb=" N3   DC I   6 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DC I   6 "    0.001 2.00e-02 2.50e+03
        pdb=" N4   DC I   6 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DC I   6 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DC I   6 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1194 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.14: 1
        2.14 -     2.83: 3202
        2.83 -     3.52: 18486
        3.52 -     4.21: 29919
        4.21 -     4.90: 44435
  Nonbonded interactions: 96043
  Sorted by model distance:
  nonbonded pdb=" O   ALA F  33 "
            pdb=" CD2 LEU F  37 "
     model   vdw
     1.451 3.460
  nonbonded pdb=" O   HIS H 109 "
            pdb=" OG  SER H 112 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" N2   DG I  58 "
            pdb=" O2   DT J -57 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" N2   DG I -60 "
            pdb=" O2   DC J  61 "
     model   vdw
     2.206 3.120
  ... (remaining 96038 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' and resid 55 through 132)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 101)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 16 through 109)
}
ncs_group {
  reference = (chain 'D' and (resid 33 through 123 or (resid 124 and (name N or name CA or nam \ 
e C or name CB or name OG ))))
  selection = (chain 'H' and resid 33 through 124)
}

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:             0.280
  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:          0.400
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     30.920
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042  11330  Z= 0.366
  Angle     :  0.740   6.252  16385  Z= 0.488
  Chirality :  0.047   0.301   1874
  Planarity :  0.003   0.019   1197
  Dihedral  : 28.574 168.307   4834
  Min Nonbonded Distance : 1.451

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.17 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.15 %
  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:  0.54 (0.31), residues: 681
  helix:  1.01 (0.22), residues: 515
  sheet:  None (None), residues: 0
  loop : -1.62 (0.42), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.002   HIS C  31 
 PHE   0.009   0.002   PHE C  25 
 TYR   0.017   0.002   TYR D  83 
 ARG   0.013   0.001   ARG F  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11044 (  706)
  hydrogen bonds       : angle       5.01185 ( 1782)
  covalent geometry    : bond        0.00713 (11330)
  covalent geometry    : angle       0.74032 (16385)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 208
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
TARDY: cannot create tardy model for: "PRO C 109 " (corrupted residue). Skipping it.
Corrupt residue: chain: C residue: PRO 109 >>> skipping
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9292 (mt0) cc_final: 0.9066 (mt0)
REVERT: A   97 GLU cc_start: 0.8443 (tt0) cc_final: 0.8191 (tt0)
REVERT: A  120 MET cc_start: 0.8495 (mtp) cc_final: 0.8030 (mtp)
REVERT: A  124 THR cc_start: 0.9775 (m) cc_final: 0.9562 (p)
REVERT: B   44 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8686 (mmmt)
REVERT: B   79 LYS cc_start: 0.9071 (mtmm) cc_final: 0.8831 (mtmm)
REVERT: B   80 THR cc_start: 0.9530 (m) cc_final: 0.9189 (p)
REVERT: B   85 ASP cc_start: 0.8843 (m-30) cc_final: 0.8592 (m-30)
REVERT: C   64 GLU cc_start: 0.8535 (tp30) cc_final: 0.8138 (tp30)
REVERT: C  104 GLN cc_start: 0.8689 (mp10) cc_final: 0.7987 (mp10)
REVERT: D   68 ASP cc_start: 0.9158 (t70) cc_final: 0.8697 (t0)
REVERT: D   71 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8783 (tm-30)
REVERT: D   85 LYS cc_start: 0.9504 (mttm) cc_final: 0.9269 (mtmm)
REVERT: E   80 THR cc_start: 0.8924 (p) cc_final: 0.8680 (p)
REVERT: E   82 LEU cc_start: 0.9401 (mt) cc_final: 0.9021 (mt)
REVERT: E  120 MET cc_start: 0.8432 (mtp) cc_final: 0.8219 (mtp)
REVERT: F   39 ARG cc_start: 0.9363 (mmt90) cc_final: 0.9163 (tpp-160)
REVERT: F   50 ILE cc_start: 0.9608 (mm) cc_final: 0.9354 (mm)
REVERT: F   52 GLU cc_start: 0.8730 (tp30) cc_final: 0.8450 (tm-30)
REVERT: G   39 TYR cc_start: 0.9215 (m-80) cc_final: 0.8934 (m-80)
REVERT: G   56 GLU cc_start: 0.9023 (tt0) cc_final: 0.8654 (tt0)
REVERT: G   57 TYR cc_start: 0.8993 (t80) cc_final: 0.8688 (t80)
REVERT: G   64 GLU cc_start: 0.8730 (tp30) cc_final: 0.8267 (tp30)
REVERT: H   46 LYS cc_start: 0.9456 (mmmt) cc_final: 0.9214 (mmmt)
REVERT: H   71 GLU cc_start: 0.9022 (tm-30) cc_final: 0.8680 (tm-30)
REVERT: H  113 GLU cc_start: 0.9257 (tp30) cc_final: 0.8774 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 208
  average time/residue: 0.2706
  time to fit residues: 74.3930
Evaluate side-chains
  158 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:   10.0000
   chunk 68 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    0.2980
   chunk 36 optimal weight:    4.9990
   chunk 70 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 81 optimal weight:    8.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B  93 GLN
D  49 HIS
** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.062914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.041084 restraints weight = 54065.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.042265 restraints weight = 28209.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.043028 restraints weight = 20224.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11330  Z= 0.174
  Angle     :  0.642   6.079  16385  Z= 0.377
  Chirality :  0.037   0.164   1874
  Planarity :  0.004   0.034   1197
  Dihedral  : 32.042 179.280   3499
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 11.40 %
    Favored  : 86.53 %
  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:  2.56 (0.31), residues: 681
  helix:  2.49 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -1.19 (0.44), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.016   0.002   PHE A  67 
 TYR   0.037   0.002   TYR D  83 
 ARG   0.007   0.001   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04560 (  706)
  hydrogen bonds       : angle       3.43261 ( 1782)
  covalent geometry    : bond        0.00380 (11330)
  covalent geometry    : angle       0.64247 (16385)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 220
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9275 (mt0) cc_final: 0.8789 (mt0)
REVERT: A   97 GLU cc_start: 0.8457 (tt0) cc_final: 0.8235 (tt0)
REVERT: A  107 THR cc_start: 0.9569 (m) cc_final: 0.9329 (p)
REVERT: A  124 THR cc_start: 0.9699 (m) cc_final: 0.9352 (p)
REVERT: A  125 GLN cc_start: 0.9203 (mt0) cc_final: 0.8391 (mp10)
REVERT: B   44 LYS cc_start: 0.8962 (mmmt) cc_final: 0.8692 (mmmt)
REVERT: B   96 THR cc_start: 0.9449 (m) cc_final: 0.9146 (p)
REVERT: C   24 GLN cc_start: 0.9318 (mm110) cc_final: 0.8895 (mp10)
REVERT: C   38 ASN cc_start: 0.8420 (t0) cc_final: 0.7982 (t0)
REVERT: C   56 GLU cc_start: 0.8528 (tt0) cc_final: 0.8260 (tt0)
REVERT: C   64 GLU cc_start: 0.8673 (tp30) cc_final: 0.8343 (tp30)
REVERT: C  104 GLN cc_start: 0.8416 (mp10) cc_final: 0.7887 (mp10)
REVERT: D   46 LYS cc_start: 0.9591 (mmtp) cc_final: 0.9278 (mmmt)
REVERT: D   68 ASP cc_start: 0.9011 (t0) cc_final: 0.8796 (t70)
REVERT: D   71 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8674 (tm-30)
REVERT: D  113 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8362 (mt-10)
REVERT: D  116 LYS cc_start: 0.9543 (ttpt) cc_final: 0.9301 (ptpp)
REVERT: D  120 LYS cc_start: 0.9514 (ttpt) cc_final: 0.9160 (ttpp)
REVERT: E  125 GLN cc_start: 0.8386 (tm-30) cc_final: 0.8136 (tm-30)
REVERT: F   52 GLU cc_start: 0.8604 (tp30) cc_final: 0.8365 (tm-30)
REVERT: F   63 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8437 (mt-10)
REVERT: F   73 THR cc_start: 0.9643 (m) cc_final: 0.9422 (p)
REVERT: F   85 ASP cc_start: 0.8853 (m-30) cc_final: 0.8552 (m-30)
REVERT: G   57 TYR cc_start: 0.8960 (t80) cc_final: 0.8442 (t80)
REVERT: G   64 GLU cc_start: 0.8740 (tp30) cc_final: 0.8166 (tp30)
REVERT: G   68 ASN cc_start: 0.9002 (m-40) cc_final: 0.8601 (m-40)
REVERT: G   84 GLN cc_start: 0.9424 (tp-100) cc_final: 0.8941 (tp-100)
REVERT: H   46 LYS cc_start: 0.9412 (mmmt) cc_final: 0.9176 (mmmt)
REVERT: H   71 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8623 (tm-30)
REVERT: H   93 GLU cc_start: 0.8615 (mp0) cc_final: 0.8221 (mp0)
REVERT: H  113 GLU cc_start: 0.9180 (tp30) cc_final: 0.8747 (tt0)
  outliers start: 12
  outliers final: 5
  residues processed: 224
  average time/residue: 0.2179
  time to fit residues: 67.7540
Evaluate side-chains
  184 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 179
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   80 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 22 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 42 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0270
   chunk 16 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 29 optimal weight:   10.0000
   chunk 19 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   overall best weight:    1.9844

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 125 GLN ** 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 = 0.3558 r_free = 0.3558 target = 0.062665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.040273 restraints weight = 55037.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.041383 restraints weight = 29882.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.042095 restraints weight = 21937.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.2690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11330  Z= 0.182
  Angle     :  0.609   7.901  16385  Z= 0.357
  Chirality :  0.035   0.145   1874
  Planarity :  0.004   0.036   1197
  Dihedral  : 31.753 177.988   3499
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 17.96 %
    Favored  : 78.76 %
  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:  2.69 (0.31), residues: 681
  helix:  2.52 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.93 (0.45), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.039   0.002   TYR D  83 
 ARG   0.008   0.001   ARG D  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04433 (  706)
  hydrogen bonds       : angle       3.30975 ( 1782)
  covalent geometry    : bond        0.00400 (11330)
  covalent geometry    : angle       0.60888 (16385)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 194
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9176 (mt0) cc_final: 0.8829 (mt0)
REVERT: A   97 GLU cc_start: 0.8440 (tt0) cc_final: 0.8219 (tt0)
REVERT: A  125 GLN cc_start: 0.9219 (mt0) cc_final: 0.8474 (mp10)
REVERT: B   85 ASP cc_start: 0.8848 (m-30) cc_final: 0.8539 (m-30)
REVERT: C   24 GLN cc_start: 0.9324 (mm110) cc_final: 0.8993 (mp10)
REVERT: C   38 ASN cc_start: 0.8299 (t0) cc_final: 0.7811 (t0)
REVERT: C   64 GLU cc_start: 0.8597 (tp30) cc_final: 0.8366 (tp30)
REVERT: C  104 GLN cc_start: 0.8499 (mp10) cc_final: 0.7906 (mp10)
REVERT: D   46 LYS cc_start: 0.9557 (mmtp) cc_final: 0.9170 (mmtt)
REVERT: D   68 ASP cc_start: 0.9096 (t70) cc_final: 0.8842 (t70)
REVERT: D   71 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8629 (tm-30)
REVERT: D  120 LYS cc_start: 0.9488 (ttpt) cc_final: 0.9137 (ttpp)
REVERT: E  123 ASP cc_start: 0.8809 (m-30) cc_final: 0.8380 (m-30)
REVERT: E  125 GLN cc_start: 0.8406 (tm-30) cc_final: 0.8068 (tm-30)
REVERT: F   39 ARG cc_start: 0.9178 (tpp-160) cc_final: 0.8611 (tpp-160)
REVERT: F   52 GLU cc_start: 0.8586 (tp30) cc_final: 0.8278 (tm-30)
REVERT: F   63 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8418 (mt-10)
REVERT: F   73 THR cc_start: 0.9610 (m) cc_final: 0.9394 (p)
REVERT: F   85 ASP cc_start: 0.8740 (m-30) cc_final: 0.8420 (m-30)
REVERT: G   38 ASN cc_start: 0.9045 (m-40) cc_final: 0.8787 (m-40)
REVERT: G   57 TYR cc_start: 0.9028 (t80) cc_final: 0.8505 (t80)
REVERT: G   64 GLU cc_start: 0.8622 (tp30) cc_final: 0.7935 (tp30)
REVERT: G   68 ASN cc_start: 0.8951 (m-40) cc_final: 0.8354 (m-40)
REVERT: G   84 GLN cc_start: 0.9405 (tp-100) cc_final: 0.8934 (tp-100)
REVERT: G   89 ASN cc_start: 0.9396 (m-40) cc_final: 0.9048 (m110)
REVERT: G   90 ASP cc_start: 0.8267 (t0) cc_final: 0.7988 (t0)
REVERT: G   92 GLU cc_start: 0.9011 (mp0) cc_final: 0.8611 (pm20)
REVERT: H   46 LYS cc_start: 0.9409 (mmmt) cc_final: 0.9159 (mmmt)
REVERT: H   71 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8601 (tm-30)
REVERT: H   93 GLU cc_start: 0.8600 (mp0) cc_final: 0.8203 (mp0)
REVERT: H  113 GLU cc_start: 0.9112 (tp30) cc_final: 0.8700 (tt0)
  outliers start: 19
  outliers final: 11
  residues processed: 201
  average time/residue: 0.2236
  time to fit residues: 63.0919
Evaluate side-chains
  192 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 181
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  101 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 89 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 75 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 81 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 48 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS
** D  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.060782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.038154 restraints weight = 55230.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.039225 restraints weight = 30670.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.039914 restraints weight = 22652.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  11330  Z= 0.273
  Angle     :  0.645   5.845  16385  Z= 0.374
  Chirality :  0.037   0.147   1874
  Planarity :  0.004   0.036   1197
  Dihedral  : 31.832 176.538   3499
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 18.48 %
    Favored  : 76.86 %
  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:  2.65 (0.31), residues: 681
  helix:  2.49 (0.21), residues: 525
  sheet:  None (None), residues: 0
  loop : -0.90 (0.44), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS B  75 
 PHE   0.014   0.002   PHE E  78 
 TYR   0.020   0.002   TYR B  88 
 ARG   0.006   0.001   ARG D  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05181 (  706)
  hydrogen bonds       : angle       3.42079 ( 1782)
  covalent geometry    : bond        0.00606 (11330)
  covalent geometry    : angle       0.64492 (16385)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 175
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9258 (mt0) cc_final: 0.8746 (mt0)
REVERT: A   97 GLU cc_start: 0.8438 (tt0) cc_final: 0.8203 (tt0)
REVERT: A  125 GLN cc_start: 0.9238 (mt0) cc_final: 0.8493 (mp10)
REVERT: B   44 LYS cc_start: 0.9092 (mmtt) cc_final: 0.8872 (tppt)
REVERT: B   84 MET cc_start: 0.9064 (tpp) cc_final: 0.8684 (mmm)
REVERT: B   88 TYR cc_start: 0.9201 (m-80) cc_final: 0.8677 (m-80)
REVERT: C   24 GLN cc_start: 0.9381 (mm110) cc_final: 0.9128 (mp10)
REVERT: C   38 ASN cc_start: 0.8351 (t0) cc_final: 0.8040 (t0)
REVERT: C   73 ASN cc_start: 0.9033 (t0) cc_final: 0.8649 (t0)
REVERT: C  104 GLN cc_start: 0.8634 (mp10) cc_final: 0.8005 (mp10)
REVERT: D   46 LYS cc_start: 0.9530 (mmtp) cc_final: 0.9243 (mmmt)
REVERT: D   68 ASP cc_start: 0.9082 (t70) cc_final: 0.8706 (t0)
REVERT: D   71 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8622 (tm-30)
REVERT: D  120 LYS cc_start: 0.9525 (ttpt) cc_final: 0.9153 (ttpp)
REVERT: E   60 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8024 (tp)
REVERT: E  105 GLU cc_start: 0.8663 (tt0) cc_final: 0.8422 (tp30)
REVERT: E  123 ASP cc_start: 0.8885 (m-30) cc_final: 0.8322 (m-30)
REVERT: E  125 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8292 (tm-30)
REVERT: F   39 ARG cc_start: 0.9176 (tpp-160) cc_final: 0.8794 (tpp-160)
REVERT: F   52 GLU cc_start: 0.8699 (tp30) cc_final: 0.8331 (tm-30)
REVERT: F   63 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8591 (mt-10)
REVERT: G   38 ASN cc_start: 0.8980 (m-40) cc_final: 0.8743 (m110)
REVERT: G   57 TYR cc_start: 0.9072 (t80) cc_final: 0.8725 (t80)
REVERT: G   64 GLU cc_start: 0.8520 (tp30) cc_final: 0.7789 (tp30)
REVERT: G   68 ASN cc_start: 0.8894 (m-40) cc_final: 0.8183 (m-40)
REVERT: G   89 ASN cc_start: 0.9404 (m-40) cc_final: 0.9010 (m110)
REVERT: G   90 ASP cc_start: 0.8515 (t0) cc_final: 0.8004 (t0)
REVERT: G   92 GLU cc_start: 0.9053 (mp0) cc_final: 0.8509 (pm20)
REVERT: H   46 LYS cc_start: 0.9439 (mmmt) cc_final: 0.9195 (mmmt)
REVERT: H   93 GLU cc_start: 0.8709 (mp0) cc_final: 0.8277 (mp0)
  outliers start: 27
  outliers final: 18
  residues processed: 186
  average time/residue: 0.2245
  time to fit residues: 58.5287
Evaluate side-chains
  186 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 167
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  131 CYS
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   87 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  101 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 48 optimal weight:   10.0000
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.062751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.039998 restraints weight = 53136.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.041015 restraints weight = 29081.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.041678 restraints weight = 21404.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11330  Z= 0.171
  Angle     :  0.597   7.110  16385  Z= 0.351
  Chirality :  0.035   0.194   1874
  Planarity :  0.004   0.045   1197
  Dihedral  : 31.596 178.311   3499
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 20.03 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.89 (0.31), residues: 681
  helix:  2.66 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.84 (0.44), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.011   0.001   PHE H  70 
 TYR   0.020   0.001   TYR B  88 
 ARG   0.006   0.000   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04239 (  706)
  hydrogen bonds       : angle       3.12581 ( 1782)
  covalent geometry    : bond        0.00374 (11330)
  covalent geometry    : angle       0.59653 (16385)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 187
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9124 (mt0) cc_final: 0.8581 (mt0)
REVERT: A   97 GLU cc_start: 0.8451 (tt0) cc_final: 0.8240 (tt0)
REVERT: A  120 MET cc_start: 0.8063 (mtm) cc_final: 0.7804 (mtm)
REVERT: A  125 GLN cc_start: 0.9190 (mt0) cc_final: 0.8448 (mp10)
REVERT: B   44 LYS cc_start: 0.9057 (mmtt) cc_final: 0.8847 (tppt)
REVERT: C   38 ASN cc_start: 0.8342 (t0) cc_final: 0.7837 (t0)
REVERT: C   73 ASN cc_start: 0.8952 (t0) cc_final: 0.8527 (t0)
REVERT: C   74 LYS cc_start: 0.9500 (mmmt) cc_final: 0.9297 (mmmt)
REVERT: C  104 GLN cc_start: 0.8496 (mp10) cc_final: 0.7992 (mp10)
REVERT: D   46 LYS cc_start: 0.9511 (mmtp) cc_final: 0.9168 (mmmt)
REVERT: D   68 ASP cc_start: 0.9087 (t70) cc_final: 0.8825 (t70)
REVERT: D   71 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8568 (tm-30)
REVERT: D  120 LYS cc_start: 0.9497 (ttpt) cc_final: 0.9148 (ttpp)
REVERT: E   79 LYS cc_start: 0.8600 (tmtt) cc_final: 0.7951 (tmtt)
REVERT: E  125 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8296 (tm-30)
REVERT: F   39 ARG cc_start: 0.9187 (tpp-160) cc_final: 0.8593 (tpp-160)
REVERT: F   52 GLU cc_start: 0.8599 (tp30) cc_final: 0.8228 (tm-30)
REVERT: F   63 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8308 (mt-10)
REVERT: G   38 ASN cc_start: 0.8941 (m-40) cc_final: 0.8641 (m110)
REVERT: G   64 GLU cc_start: 0.8427 (tp30) cc_final: 0.7651 (tp30)
REVERT: G   68 ASN cc_start: 0.8892 (m-40) cc_final: 0.8014 (m-40)
REVERT: G   84 GLN cc_start: 0.9395 (tp-100) cc_final: 0.9133 (tp-100)
REVERT: G   89 ASN cc_start: 0.9407 (m-40) cc_final: 0.9019 (m110)
REVERT: G   90 ASP cc_start: 0.8416 (t0) cc_final: 0.7875 (t0)
REVERT: G   92 GLU cc_start: 0.8999 (mp0) cc_final: 0.8477 (pm20)
REVERT: H   46 LYS cc_start: 0.9408 (mmmt) cc_final: 0.9139 (mmmt)
  outliers start: 17
  outliers final: 13
  residues processed: 195
  average time/residue: 0.2253
  time to fit residues: 61.4455
Evaluate side-chains
  187 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 174
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   88 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  101 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 77 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 58 optimal weight:    0.4980
   chunk 73 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 44 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   overall best weight:    4.2988

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 HIS
E  55 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.061478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.038641 restraints weight = 54860.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.039701 restraints weight = 30381.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.040376 restraints weight = 22403.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  11330  Z= 0.247
  Angle     :  0.634   6.834  16385  Z= 0.368
  Chirality :  0.036   0.174   1874
  Planarity :  0.004   0.042   1197
  Dihedral  : 31.681 178.712   3499
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 23.14 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.75 (0.31), residues: 681
  helix:  2.54 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -0.80 (0.44), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS B  75 
 PHE   0.010   0.002   PHE B  61 
 TYR   0.018   0.002   TYR C  57 
 ARG   0.006   0.001   ARG D  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04862 (  706)
  hydrogen bonds       : angle       3.26628 ( 1782)
  covalent geometry    : bond        0.00548 (11330)
  covalent geometry    : angle       0.63406 (16385)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 168
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9166 (mt0) cc_final: 0.8740 (mt0)
REVERT: A   97 GLU cc_start: 0.8470 (tt0) cc_final: 0.8263 (tt0)
REVERT: C   38 ASN cc_start: 0.8304 (t0) cc_final: 0.7857 (t0)
REVERT: C   73 ASN cc_start: 0.8966 (t0) cc_final: 0.8512 (t0)
REVERT: C  104 GLN cc_start: 0.8659 (mp10) cc_final: 0.8057 (mp10)
REVERT: D   46 LYS cc_start: 0.9499 (mmtp) cc_final: 0.9128 (mmmt)
REVERT: D   68 ASP cc_start: 0.9060 (t70) cc_final: 0.8726 (t0)
REVERT: D   71 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8588 (tm-30)
REVERT: D  120 LYS cc_start: 0.9520 (ttpt) cc_final: 0.9153 (ttpp)
REVERT: E   79 LYS cc_start: 0.8765 (tmtt) cc_final: 0.8110 (tmtt)
REVERT: E  123 ASP cc_start: 0.8796 (m-30) cc_final: 0.8276 (m-30)
REVERT: E  125 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8348 (tm-30)
REVERT: E  129 TYR cc_start: 0.8554 (t80) cc_final: 0.8334 (t80)
REVERT: F   39 ARG cc_start: 0.9179 (tpp-160) cc_final: 0.8727 (tpp-160)
REVERT: F   63 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8519 (mt-10)
REVERT: F   85 ASP cc_start: 0.8472 (m-30) cc_final: 0.8198 (m-30)
REVERT: G   38 ASN cc_start: 0.8996 (m-40) cc_final: 0.8701 (m110)
REVERT: G   57 TYR cc_start: 0.8959 (t80) cc_final: 0.8718 (t80)
REVERT: G   64 GLU cc_start: 0.8406 (tp30) cc_final: 0.7674 (tp30)
REVERT: G   68 ASN cc_start: 0.8835 (m-40) cc_final: 0.7955 (m-40)
REVERT: G   89 ASN cc_start: 0.9420 (m-40) cc_final: 0.9022 (m110)
REVERT: G   90 ASP cc_start: 0.8522 (t0) cc_final: 0.7906 (t0)
REVERT: G   92 GLU cc_start: 0.9045 (mp0) cc_final: 0.8471 (pm20)
REVERT: H   46 LYS cc_start: 0.9438 (mmmt) cc_final: 0.9180 (mmmt)
REVERT: H   93 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8221 (mm-30)
REVERT: H  109 HIS cc_start: 0.9283 (OUTLIER) cc_final: 0.8605 (m-70)
  outliers start: 19
  outliers final: 15
  residues processed: 178
  average time/residue: 0.2454
  time to fit residues: 61.3851
Evaluate side-chains
  181 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 165
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  109 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 89 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 41 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 44 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 11 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    3.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  55 GLN
E 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.061853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.039041 restraints weight = 54725.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.040086 restraints weight = 29657.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.040769 restraints weight = 21833.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11330  Z= 0.221
  Angle     :  0.630   8.650  16385  Z= 0.365
  Chirality :  0.036   0.181   1874
  Planarity :  0.004   0.044   1197
  Dihedral  : 31.645 179.583   3499
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 23.14 %
    Favored  : 73.23 %
  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:  2.78 (0.31), residues: 681
  helix:  2.54 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -0.70 (0.45), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.011   0.001   PHE B  61 
 TYR   0.015   0.001   TYR H  83 
 ARG   0.004   0.000   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04525 (  706)
  hydrogen bonds       : angle       3.20908 ( 1782)
  covalent geometry    : bond        0.00491 (11330)
  covalent geometry    : angle       0.62970 (16385)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 174
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 GLN cc_start: 0.9166 (mt0) cc_final: 0.8621 (mt0)
REVERT: A   97 GLU cc_start: 0.8474 (tt0) cc_final: 0.8268 (tt0)
REVERT: B   88 TYR cc_start: 0.9036 (m-80) cc_final: 0.8828 (m-80)
REVERT: C   73 ASN cc_start: 0.8966 (t0) cc_final: 0.8507 (t0)
REVERT: C  104 GLN cc_start: 0.8662 (mp10) cc_final: 0.8055 (mp10)
REVERT: D   46 LYS cc_start: 0.9483 (mmtp) cc_final: 0.9002 (mmmt)
REVERT: D   68 ASP cc_start: 0.9064 (t70) cc_final: 0.8769 (t70)
REVERT: D   71 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8592 (tm-30)
REVERT: D  120 LYS cc_start: 0.9515 (ttpt) cc_final: 0.9150 (ttpp)
REVERT: E   79 LYS cc_start: 0.8683 (tmtt) cc_final: 0.7977 (tmtt)
REVERT: E   80 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8399 (t)
REVERT: E  123 ASP cc_start: 0.8822 (m-30) cc_final: 0.8275 (m-30)
REVERT: E  125 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8374 (tm-30)
REVERT: F   39 ARG cc_start: 0.9177 (tpp-160) cc_final: 0.8731 (tpp-160)
REVERT: F   63 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8485 (mt-10)
REVERT: F   85 ASP cc_start: 0.8506 (m-30) cc_final: 0.8218 (m-30)
REVERT: F   88 TYR cc_start: 0.9151 (m-10) cc_final: 0.8892 (m-10)
REVERT: G   57 TYR cc_start: 0.8972 (t80) cc_final: 0.8657 (t80)
REVERT: G   64 GLU cc_start: 0.8363 (tp30) cc_final: 0.7694 (tp30)
REVERT: G   68 ASN cc_start: 0.8830 (m-40) cc_final: 0.8153 (m-40)
REVERT: G   89 ASN cc_start: 0.9442 (m-40) cc_final: 0.9027 (m110)
REVERT: G   90 ASP cc_start: 0.8520 (t0) cc_final: 0.7893 (t0)
REVERT: G   92 GLU cc_start: 0.9045 (mp0) cc_final: 0.8492 (pm20)
REVERT: H   46 LYS cc_start: 0.9436 (mmmt) cc_final: 0.9174 (mmmt)
REVERT: H   93 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8197 (mm-30)
REVERT: H  109 HIS cc_start: 0.9277 (OUTLIER) cc_final: 0.8621 (m-70)
  outliers start: 21
  outliers final: 17
  residues processed: 186
  average time/residue: 0.2302
  time to fit residues: 60.0986
Evaluate side-chains
  185 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 166
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   66 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  109 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 43 optimal weight:    0.0870
   chunk 47 optimal weight:    1.9990
   chunk 55 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 49 optimal weight:    8.9990
   chunk 40 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   overall best weight:    2.0166

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN
G  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.062801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.040029 restraints weight = 54242.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.041125 restraints weight = 29651.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.041832 restraints weight = 21773.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.3724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11330  Z= 0.179
  Angle     :  0.624   9.631  16385  Z= 0.360
  Chirality :  0.035   0.170   1874
  Planarity :  0.003   0.045   1197
  Dihedral  : 31.495 178.438   3499
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 24.01 %
    Favored  : 73.06 %
  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:  2.84 (0.31), residues: 681
  helix:  2.59 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -0.70 (0.45), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.019   0.002   TYR H  83 
 ARG   0.004   0.000   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04207 (  706)
  hydrogen bonds       : angle       3.12232 ( 1782)
  covalent geometry    : bond        0.00397 (11330)
  covalent geometry    : angle       0.62368 (16385)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 184
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.9183 (tptp) cc_final: 0.8834 (tptt)
REVERT: A   85 GLN cc_start: 0.9082 (mt0) cc_final: 0.8639 (mt0)
REVERT: C   73 ASN cc_start: 0.8975 (t0) cc_final: 0.8554 (t0)
REVERT: C   74 LYS cc_start: 0.9529 (mmmt) cc_final: 0.9178 (mmmt)
REVERT: C  104 GLN cc_start: 0.8621 (mp10) cc_final: 0.8024 (mp10)
REVERT: D   46 LYS cc_start: 0.9469 (mmtp) cc_final: 0.9089 (mmmt)
REVERT: D   68 ASP cc_start: 0.9095 (t70) cc_final: 0.8832 (t70)
REVERT: D   71 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8591 (tm-30)
REVERT: D   83 TYR cc_start: 0.8515 (t80) cc_final: 0.8236 (t80)
REVERT: D  120 LYS cc_start: 0.9477 (ttpt) cc_final: 0.9121 (ttpp)
REVERT: E   79 LYS cc_start: 0.8633 (tmtt) cc_final: 0.7926 (tmtt)
REVERT: E  123 ASP cc_start: 0.8797 (m-30) cc_final: 0.8331 (m-30)
REVERT: E  125 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8379 (tm-30)
REVERT: F   39 ARG cc_start: 0.9179 (tpp-160) cc_final: 0.8592 (tpp-160)
REVERT: F   63 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8492 (mt-10)
REVERT: F   88 TYR cc_start: 0.9133 (m-10) cc_final: 0.8867 (m-10)
REVERT: G   57 TYR cc_start: 0.8958 (t80) cc_final: 0.8425 (t80)
REVERT: G   64 GLU cc_start: 0.8361 (tp30) cc_final: 0.7718 (tp30)
REVERT: G   68 ASN cc_start: 0.8869 (m-40) cc_final: 0.8075 (m-40)
REVERT: G   89 ASN cc_start: 0.9410 (m-40) cc_final: 0.9033 (m110)
REVERT: G   90 ASP cc_start: 0.8463 (t0) cc_final: 0.7861 (t0)
REVERT: G   92 GLU cc_start: 0.9022 (mp0) cc_final: 0.8474 (pm20)
REVERT: H   46 LYS cc_start: 0.9452 (mmmt) cc_final: 0.9166 (mmmt)
REVERT: H   93 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8147 (mm-30)
REVERT: H  109 HIS cc_start: 0.9253 (OUTLIER) cc_final: 0.8590 (m-70)
REVERT: H  113 GLU cc_start: 0.9226 (tp30) cc_final: 0.8869 (tt0)
  outliers start: 17
  outliers final: 14
  residues processed: 193
  average time/residue: 0.2666
  time to fit residues: 71.8056
Evaluate side-chains
  192 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 177
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  109 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 81 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 63 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 82 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    1.6982

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN
E  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.063071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.040468 restraints weight = 54725.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.041540 restraints weight = 29886.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.042250 restraints weight = 21964.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.3897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11330  Z= 0.172
  Angle     :  0.615   8.365  16385  Z= 0.358
  Chirality :  0.034   0.163   1874
  Planarity :  0.004   0.043   1197
  Dihedral  : 31.416 177.839   3499
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 24.70 %
    Favored  : 72.88 %
  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:  2.94 (0.32), residues: 681
  helix:  2.64 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -0.60 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.009   0.001   PHE B  61 
 TYR   0.019   0.002   TYR C  57 
 ARG   0.004   0.000   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04190 (  706)
  hydrogen bonds       : angle       3.06168 ( 1782)
  covalent geometry    : bond        0.00380 (11330)
  covalent geometry    : angle       0.61543 (16385)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 198
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.9172 (tptp) cc_final: 0.8810 (tptt)
REVERT: A   85 GLN cc_start: 0.9067 (mt0) cc_final: 0.8633 (mt0)
REVERT: A  125 GLN cc_start: 0.9131 (mt0) cc_final: 0.8807 (mt0)
REVERT: C   73 ASN cc_start: 0.8965 (t0) cc_final: 0.8546 (t0)
REVERT: C   74 LYS cc_start: 0.9536 (mmmt) cc_final: 0.9193 (mmmt)
REVERT: C  104 GLN cc_start: 0.8590 (mp10) cc_final: 0.7914 (mp10)
REVERT: D   46 LYS cc_start: 0.9477 (mmtp) cc_final: 0.9028 (mmmt)
REVERT: D   68 ASP cc_start: 0.9086 (t70) cc_final: 0.8836 (t70)
REVERT: D   71 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8584 (tm-30)
REVERT: D   83 TYR cc_start: 0.8448 (t80) cc_final: 0.8162 (t80)
REVERT: D  120 LYS cc_start: 0.9471 (ttpt) cc_final: 0.9114 (ttpp)
REVERT: E   65 LEU cc_start: 0.9523 (tt) cc_final: 0.9264 (tt)
REVERT: E   79 LYS cc_start: 0.8660 (tmtt) cc_final: 0.8002 (tmtt)
REVERT: E   80 THR cc_start: 0.8933 (p) cc_final: 0.8458 (t)
REVERT: E   82 LEU cc_start: 0.9203 (mt) cc_final: 0.8992 (mt)
REVERT: E  125 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8361 (tm-30)
REVERT: F   39 ARG cc_start: 0.9187 (tpp-160) cc_final: 0.8597 (tpp-160)
REVERT: F   63 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8476 (mt-10)
REVERT: F   88 TYR cc_start: 0.9085 (m-10) cc_final: 0.8790 (m-10)
REVERT: G   57 TYR cc_start: 0.8944 (t80) cc_final: 0.8365 (t80)
REVERT: G   89 ASN cc_start: 0.9463 (m-40) cc_final: 0.9110 (m110)
REVERT: G   90 ASP cc_start: 0.8483 (t0) cc_final: 0.7889 (t0)
REVERT: G   92 GLU cc_start: 0.9008 (mp0) cc_final: 0.8495 (pm20)
REVERT: H   46 LYS cc_start: 0.9447 (mmmt) cc_final: 0.9164 (mmmt)
REVERT: H   93 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8122 (mm-30)
REVERT: H  109 HIS cc_start: 0.9241 (OUTLIER) cc_final: 0.8597 (m-70)
REVERT: H  113 GLU cc_start: 0.9191 (tp30) cc_final: 0.8828 (tt0)
  outliers start: 14
  outliers final: 10
  residues processed: 204
  average time/residue: 0.2189
  time to fit residues: 62.7997
Evaluate side-chains
  194 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 183
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue  100 LEU
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   61 GLU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  109 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 13 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 83 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   chunk 70 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 58 optimal weight:    7.9990
   chunk 46 optimal weight:    4.9990
   overall best weight:    3.3986

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN
G  84 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.062265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.039485 restraints weight = 54771.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.040554 restraints weight = 30302.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.041244 restraints weight = 22435.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.3926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  11330  Z= 0.218
  Angle     :  0.647  12.060  16385  Z= 0.371
  Chirality :  0.036   0.169   1874
  Planarity :  0.004   0.042   1197
  Dihedral  : 31.454 179.731   3499
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 25.56 %
    Favored  : 71.68 %
  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:  2.83 (0.32), residues: 681
  helix:  2.57 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -0.64 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.013   0.001   PHE A  67 
 TYR   0.020   0.002   TYR H  83 
 ARG   0.004   0.000   ARG D  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04585 (  706)
  hydrogen bonds       : angle       3.16125 ( 1782)
  covalent geometry    : bond        0.00487 (11330)
  covalent geometry    : angle       0.64674 (16385)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 177
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 LYS cc_start: 0.9165 (tptp) cc_final: 0.8645 (tmtt)
REVERT: A   85 GLN cc_start: 0.9086 (mt0) cc_final: 0.8613 (mt0)
REVERT: C   73 ASN cc_start: 0.8996 (t0) cc_final: 0.8583 (t0)
REVERT: C   74 LYS cc_start: 0.9529 (mmmt) cc_final: 0.9185 (mmmt)
REVERT: C  104 GLN cc_start: 0.8660 (mp10) cc_final: 0.7948 (mp10)
REVERT: D   46 LYS cc_start: 0.9472 (mmtp) cc_final: 0.9033 (mmmt)
REVERT: D   68 ASP cc_start: 0.9055 (t70) cc_final: 0.8760 (t70)
REVERT: D   71 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8576 (tm-30)
REVERT: D   83 TYR cc_start: 0.8503 (t80) cc_final: 0.8205 (t80)
REVERT: D  120 LYS cc_start: 0.9516 (ttpt) cc_final: 0.9156 (ttpp)
REVERT: E   65 LEU cc_start: 0.9559 (tt) cc_final: 0.9300 (tt)
REVERT: E   79 LYS cc_start: 0.8778 (tmtt) cc_final: 0.8116 (tmtt)
REVERT: E   82 LEU cc_start: 0.9281 (mt) cc_final: 0.9030 (mt)
REVERT: E  123 ASP cc_start: 0.8804 (m-30) cc_final: 0.8237 (m-30)
REVERT: E  125 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8417 (tm-30)
REVERT: F   39 ARG cc_start: 0.9186 (tpp-160) cc_final: 0.8602 (tpp-160)
REVERT: F   63 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8516 (mt-10)
REVERT: F   88 TYR cc_start: 0.9151 (m-10) cc_final: 0.8840 (m-10)
REVERT: G   57 TYR cc_start: 0.8971 (t80) cc_final: 0.8534 (t80)
REVERT: G   59 THR cc_start: 0.9615 (m) cc_final: 0.9279 (t)
REVERT: G   89 ASN cc_start: 0.9467 (m-40) cc_final: 0.9130 (m110)
REVERT: G   90 ASP cc_start: 0.8512 (t0) cc_final: 0.7924 (t0)
REVERT: G   92 GLU cc_start: 0.9052 (mp0) cc_final: 0.8550 (pm20)
REVERT: H   46 LYS cc_start: 0.9438 (mmmt) cc_final: 0.9167 (mmmt)
REVERT: H   93 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8221 (mm-30)
REVERT: H  109 HIS cc_start: 0.9269 (OUTLIER) cc_final: 0.8627 (m-70)
REVERT: H  113 GLU cc_start: 0.9235 (tp30) cc_final: 0.8886 (tt0)
  outliers start: 16
  outliers final: 12
  residues processed: 185
  average time/residue: 0.2784
  time to fit residues: 73.2785
Evaluate side-chains
  186 residues out of total 579 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 173
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain C residue   63 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  109 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 49 optimal weight:    9.9990
   chunk 71 optimal weight:   10.0000
   chunk 79 optimal weight:    9.9990
   chunk 68 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 81 optimal weight:   10.0000
   overall best weight:    2.9186

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

Flipped N/Q/H residues before XYZ refinement:
E  55 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.062320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2886 r_free = 0.2886 target = 0.040260 restraints weight = 53453.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.041355 restraints weight = 29194.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.042044 restraints weight = 21411.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.2888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.4040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11330  Z= 0.202
  Angle     :  0.639  10.990  16385  Z= 0.368
  Chirality :  0.036   0.184   1874
  Planarity :  0.004   0.042   1197
  Dihedral  : 31.401 179.894   3499
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 26.25 %
    Favored  : 71.16 %
  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:  2.77 (0.32), residues: 681
  helix:  2.54 (0.22), residues: 525
  sheet:  None (None), residues: 0
  loop : -0.69 (0.46), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  75 
 PHE   0.019   0.001   PHE A  67 
 TYR   0.019   0.002   TYR H  83 
 ARG   0.003   0.000   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04418 (  706)
  hydrogen bonds       : angle       3.16325 ( 1782)
  covalent geometry    : bond        0.00449 (11330)
  covalent geometry    : angle       0.63870 (16385)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3470.06 seconds
wall clock time: 61 minutes 56.96 seconds (3716.96 seconds total)