Starting phenix.real_space_refine
on Mon Jul 28 11:41:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d69_30591/07_2025/7d69_30591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d69_30591/07_2025/7d69_30591.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7d69_30591/07_2025/7d69_30591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d69_30591/07_2025/7d69_30591.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d69_30591/07_2025/7d69_30591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d69_30591/07_2025/7d69_30591.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     250      5.49       5
     S      13      5.16       5
     C    6015      2.51       5
     N    2012      2.21       5
     O    2567      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 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: 10857
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 716
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 3, 'TRANS': 86}
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "D"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 743
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 1, 'TRANS': 94}
    Chain: "E"
      Number of atoms: 779
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 779
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 95}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "F"
      Number of atoms: 621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 621
          Classifications: {'peptide': 78}
          Incomplete info: {'n_c_alpha_c_only': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 743
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 1, 'TRANS': 94}
    Chain: "C"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 754
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "G"
      Number of atoms: 754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 754
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2561
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2561
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
    Chain: "J"
      Number of atoms: 2564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 2564
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
  Time building chain proxies: 6.73, per 1000 atoms: 0.62
  Number of scatterers: 10857
  At special positions: 0
  Unit cell: (84, 121.8, 114.45, 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      13     16.00
     P     250     15.00
     O    2567      8.00
     N    2012      7.00
     C    6015      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.67
  Conformation dependent library (CDL) restraints added in 680.4 milliseconds
  

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1368

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 6 sheets defined
      74.0% alpha, 1.9% beta
      121 base pairs and 227 stacking pairs defined.
    Time for finding SS restraints: 5.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 51 through 58
      removed outlier: 3.897A  pdb=" N   TYR A  55 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 78
    Processing helix  chain 'A' and resid 88 through 117
    Processing helix  chain 'A' and resid 123 through 133
    Processing helix  chain 'B' and resid 21 through 25
    Processing helix  chain 'B' and resid 26 through 37
    Processing helix  chain 'B' and resid 45 through 72
      removed outlier: 3.698A  pdb=" N   GLY B  72 " --> pdb=" O   TYR B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 78 through 90
    Processing helix  chain 'D' and resid 30 through 45
      removed outlier: 3.607A  pdb=" N   ILE D  43 " --> pdb=" O   ARG D  39 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ARG D  44 " --> pdb=" O   SER D  40 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 84
    Processing helix  chain 'D' and resid 89 through 101
    Processing helix  chain 'D' and resid 103 through 122
    Processing helix  chain 'E' and resid 45 through 58
      removed outlier: 4.096A  pdb=" N   VAL E  49 " --> pdb=" O   GLY E  45 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   LYS E  50 " --> pdb=" O   MET E  46 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   SER E  58 " --> pdb=" O   LYS E  54 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 79
    Processing helix  chain 'E' and resid 88 through 117
    Processing helix  chain 'E' and resid 123 through 133
    Processing helix  chain 'F' and resid 21 through 25
    Processing helix  chain 'F' and resid 26 through 38
    Processing helix  chain 'F' and resid 44 through 72
      removed outlier: 4.273A  pdb=" N   GLN F  48 " --> pdb=" O   SER F  44 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ALA F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   GLY F  72 " --> pdb=" O   TYR F  68 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 78 through 88
    Processing helix  chain 'H' and resid 30 through 43
    Processing helix  chain 'H' and resid 54 through 84
    Processing helix  chain 'H' and resid 89 through 101
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'C' and resid 13 through 18
    Processing helix  chain 'C' and resid 23 through 34
    Processing helix  chain 'C' and resid 42 through 68
      removed outlier: 4.162A  pdb=" N   VAL C  46 " --> pdb=" O   SER C  42 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 87
      removed outlier: 3.604A  pdb=" N   ASP C  87 " --> pdb=" O   ALA C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 94
    Processing helix  chain 'G' and resid 13 through 18
    Processing helix  chain 'G' and resid 23 through 34
    Processing helix  chain 'G' and resid 43 through 68
      removed outlier: 3.618A  pdb=" N   TYR G  47 " --> pdb=" O   ASP G  43 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 76 through 87
      removed outlier: 4.103A  pdb=" N   ASP G  87 " --> pdb=" O   ALA G  83 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 87 through 94
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 87
      removed outlier: 7.028A  pdb=" N   ARG A  86 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 122
    Processing sheet with id=AA3, first strand: chain 'B' and resid 93 through 94
      removed outlier: 3.681A  pdb=" N   TYR B  94 " --> pdb=" O   THR G  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'E' and resid 86 through 87
      removed outlier: 7.127A  pdb=" N   ARG E  86 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 121 through 122
    Processing sheet with id=AA6, first strand: chain 'F' and resid 92 through 94
      removed outlier: 6.189A  pdb=" N   THR F  92 " --> pdb=" O   THR C  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6

    392 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      315 hydrogen bonds
      630 hydrogen bond angles
      0 basepair planarities
      121 basepair parallelities
      227 stacking parallelities
  Total time for adding SS restraints: 3.91

  Time building geometry restraints manager: 3.16 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: 1840
        1.33 -     1.45: 3827
        1.45 -     1.57: 5355
        1.57 -     1.68: 498
        1.68 -     1.80: 22
  Bond restraints: 11542
  Sorted by residual:
  bond pdb=" CG1 ILE G  24 "
       pdb=" CD1 ILE G  24 "
    ideal  model  delta    sigma   weight residual
    1.513  1.430  0.083 3.90e-02 6.57e+02 4.50e+00
  bond pdb=" CG  GLN B  89 "
       pdb=" CD  GLN B  89 "
    ideal  model  delta    sigma   weight residual
    1.516  1.473  0.043 2.50e-02 1.60e+03 2.89e+00
  bond pdb=" CB  VAL A  76 "
       pdb=" CG1 VAL A  76 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.86e+00
  bond pdb=" CG  LEU F  86 "
       pdb=" CD1 LEU F  86 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.49e+00
  bond pdb=" CB  VAL D  37 "
       pdb=" CG1 VAL D  37 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.49e+00
  ... (remaining 11537 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 15163
        1.54 -     3.07: 1325
        3.07 -     4.61: 121
        4.61 -     6.14: 19
        6.14 -     7.68: 9
  Bond angle restraints: 16637
  Sorted by residual:
  angle pdb=" C3'  DT J 114 "
        pdb=" O3'  DT J 114 "
        pdb=" P    DC J 115 "
      ideal   model   delta    sigma   weight residual
     120.20  125.46   -5.26 1.50e+00 4.44e-01 1.23e+01
  angle pdb=" C3'  DT I 120 "
        pdb=" O3'  DT I 120 "
        pdb=" P    DC I 121 "
      ideal   model   delta    sigma   weight residual
     120.20  124.81   -4.61 1.50e+00 4.44e-01 9.45e+00
  angle pdb=" O4'  DA I 113 "
        pdb=" C1'  DA I 113 "
        pdb=" N9   DA I 113 "
      ideal   model   delta    sigma   weight residual
     108.40  104.02    4.38 1.50e+00 4.44e-01 8.51e+00
  angle pdb=" C4'  DA I  72 "
        pdb=" C3'  DA I  72 "
        pdb=" O3'  DA I  72 "
      ideal   model   delta    sigma   weight residual
     110.00  105.80    4.20 1.50e+00 4.44e-01 7.83e+00
  angle pdb=" O4'  DG J  11 "
        pdb=" C1'  DG J  11 "
        pdb=" C2'  DG J  11 "
      ideal   model   delta    sigma   weight residual
     106.40  102.23    4.17 1.50e+00 4.44e-01 7.72e+00
  ... (remaining 16632 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.69: 4776
       30.69 -    61.37: 1489
       61.37 -    92.05: 46
       92.05 -   122.74: 8
      122.74 -   153.42: 4
  Dihedral angle restraints: 6323
    sinusoidal: 4214
      harmonic: 2109
  Sorted by residual:
  dihedral pdb=" C4'  DT I 120 "
           pdb=" C3'  DT I 120 "
           pdb=" O3'  DT I 120 "
           pdb=" P    DC I 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   66.58  153.42     1      3.50e+01 8.16e-04 1.48e+01
  dihedral pdb=" C4'  DT J 114 "
           pdb=" C3'  DT J 114 "
           pdb=" O3'  DT J 114 "
           pdb=" P    DC J 115 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   76.89  143.11     1      3.50e+01 8.16e-04 1.41e+01
  dihedral pdb=" C4'  DC I 100 "
           pdb=" C3'  DC I 100 "
           pdb=" O3'  DC I 100 "
           pdb=" P    DT I 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   94.95  125.05     1      3.50e+01 8.16e-04 1.23e+01
  ... (remaining 6320 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1230
       0.048 -    0.095: 510
       0.095 -    0.143: 142
       0.143 -    0.190: 19
       0.190 -    0.237: 1
  Chirality restraints: 1902
  Sorted by residual:
  chirality pdb=" C3'  DT J 114 "
            pdb=" C4'  DT J 114 "
            pdb=" O3'  DT J 114 "
            pdb=" C2'  DT J 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.42   -0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CB  THR G  98 "
            pdb=" CA  THR G  98 "
            pdb=" OG1 THR G  98 "
            pdb=" CG2 THR G  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.37    0.19 2.00e-01 2.50e+01 8.63e-01
  chirality pdb=" C4'  DA I  83 "
            pdb=" C5'  DA I  83 "
            pdb=" O4'  DA I  83 "
            pdb=" C3'  DA I  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.34   -0.19 2.00e-01 2.50e+01 8.59e-01
  ... (remaining 1899 not shown)

  Planarity restraints: 1240
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I   9 "   -0.036 2.00e-02 2.50e+03   1.88e-02 7.92e+00
        pdb=" N1   DC I   9 "    0.039 2.00e-02 2.50e+03
        pdb=" C2   DC I   9 "   -0.005 2.00e-02 2.50e+03
        pdb=" O2   DC I   9 "    0.009 2.00e-02 2.50e+03
        pdb=" N3   DC I   9 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DC I   9 "   -0.004 2.00e-02 2.50e+03
        pdb=" N4   DC I   9 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5   DC I   9 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DC I   9 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J   9 "   -0.024 2.00e-02 2.50e+03   1.78e-02 7.11e+00
        pdb=" N1   DC J   9 "    0.044 2.00e-02 2.50e+03
        pdb=" C2   DC J   9 "   -0.017 2.00e-02 2.50e+03
        pdb=" O2   DC J   9 "    0.007 2.00e-02 2.50e+03
        pdb=" N3   DC J   9 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DC J   9 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4   DC J   9 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DC J   9 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DC J   9 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  31 "   -0.038 2.00e-02 2.50e+03   1.60e-02 7.00e+00
        pdb=" N9   DA I  31 "    0.029 2.00e-02 2.50e+03
        pdb=" C8   DA I  31 "    0.014 2.00e-02 2.50e+03
        pdb=" N7   DA I  31 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  31 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6   DA I  31 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  31 "   -0.013 2.00e-02 2.50e+03
        pdb=" N1   DA I  31 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2   DA I  31 "    0.007 2.00e-02 2.50e+03
        pdb=" N3   DA I  31 "    0.008 2.00e-02 2.50e+03
        pdb=" C4   DA I  31 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1237 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 186
        2.63 -     3.20: 9662
        3.20 -     3.76: 21647
        3.76 -     4.33: 27367
        4.33 -     4.90: 38963
  Nonbonded interactions: 97825
  Sorted by model distance:
  nonbonded pdb=" OG  SER E  69 "
            pdb=" NH1 ARG E  73 "
     model   vdw
     2.062 3.120
  nonbonded pdb=" N   ASN D  55 "
            pdb=" OP1  DA I  12 "
     model   vdw
     2.134 3.120
  nonbonded pdb=" OG  SER C  41 "
            pdb=" OP1  DG J  98 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" OH  TYR F  68 "
            pdb=" OE2 GLU H  75 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" N2   DG I 114 "
            pdb=" O2   DT J  13 "
     model   vdw
     2.210 3.120
  ... (remaining 97820 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 51 through 140)
}
ncs_group {
  reference = (chain 'B' and (resid 20 through 96 or (resid 97 and (name N or name CA or name  \ 
C ))))
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and (resid 7 through 65 or resid 67 through 125))
  selection = (chain 'J' and (resid 1 through 59 or resid 61 through 119))
}

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:             0.450
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     30.190
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
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      :  0.009   0.083  11542  Z= 0.376
  Angle     :  0.883   7.680  16637  Z= 0.522
  Chirality :  0.054   0.237   1902
  Planarity :  0.005   0.042   1240
  Dihedral  : 28.860 153.423   4955
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 19.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.18 (0.29), residues: 711
  helix: -0.22 (0.21), residues: 513
  sheet:  None (None), residues: 0
  loop : -2.04 (0.40), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.016   0.002   HIS G  79 
 PHE   0.025   0.004   PHE C  94 
 TYR   0.020   0.003   TYR C  47 
 ARG   0.013   0.001   ARG A  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09313 (  707)
  hydrogen bonds       : angle       4.46578 ( 1794)
  covalent geometry    : bond        0.00886 (11542)
  covalent geometry    : angle       0.88264 (16637)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7769 (mp0)
REVERT: B   35 ARG cc_start: 0.8081 (mtt-85) cc_final: 0.7724 (mtt90)
REVERT: D   78 ASN cc_start: 0.8833 (t0) cc_final: 0.8304 (t0)
REVERT: D   82 ILE cc_start: 0.9136 (mt) cc_final: 0.8678 (mt)
REVERT: F   31 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8033 (mmm160)
REVERT: F   87 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8581 (ttmt)
REVERT: H   51 LEU cc_start: 0.7360 (pp) cc_final: 0.7109 (pp)
REVERT: C   96 ASN cc_start: 0.8080 (p0) cc_final: 0.7802 (p0)
REVERT: C  101 GLU cc_start: 0.8246 (mt-10) cc_final: 0.7940 (mt-10)
REVERT: G   85 ARG cc_start: 0.7539 (mtt180) cc_final: 0.7337 (mtt180)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.3765
  time to fit residues: 60.7133
Evaluate side-chains
  100 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:   10.0000
   chunk 69 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 72 optimal weight:    8.9990
   chunk 27 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 83 optimal weight:    8.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 GLN
E  44 GLN
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.182345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.125449 restraints weight = 14638.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.126933 restraints weight = 9779.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.127306 restraints weight = 9365.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  11542  Z= 0.173
  Angle     :  0.636   6.431  16637  Z= 0.373
  Chirality :  0.038   0.170   1902
  Planarity :  0.005   0.059   1240
  Dihedral  : 31.892 177.650   3513
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.08 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.42 (0.29), residues: 711
  helix:  0.90 (0.21), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.32 (0.42), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.015   0.002   HIS G  79 
 PHE   0.021   0.002   PHE G  60 
 TYR   0.013   0.001   TYR E  55 
 ARG   0.004   0.001   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03995 (  707)
  hydrogen bonds       : angle       3.43993 ( 1794)
  covalent geometry    : bond        0.00391 (11542)
  covalent geometry    : angle       0.63644 (16637)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 LYS cc_start: 0.8001 (mttp) cc_final: 0.7796 (mttp)
REVERT: B   35 ARG cc_start: 0.7798 (mtt-85) cc_final: 0.7538 (mtt90)
REVERT: F   31 ARG cc_start: 0.8319 (mmm-85) cc_final: 0.8028 (mmm160)
REVERT: F   51 ARG cc_start: 0.8181 (mtt180) cc_final: 0.7908 (mtt-85)
REVERT: F   87 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8532 (ttmt)
REVERT: H   41 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8078 (tm-30)
REVERT: H   84 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7787 (mmtt)
REVERT: H   98 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8395 (ttmm)
REVERT: C  101 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7803 (mt-10)
REVERT: G   62 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7361 (mm-30)
  outliers start: 10
  outliers final: 3
  residues processed: 120
  average time/residue: 0.3043
  time to fit residues: 48.4228
Evaluate side-chains
  98 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 95
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue  104 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 80 optimal weight:   20.0000
   chunk 63 optimal weight:    0.8980
   chunk 18 optimal weight:   10.0000
   chunk 58 optimal weight:    6.9990
   chunk 88 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 85 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0570
   overall best weight:    1.5702

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  30 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.181233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.124941 restraints weight = 15052.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.125364 restraints weight = 10345.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.126373 restraints weight = 9752.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  11542  Z= 0.188
  Angle     :  0.611   6.676  16637  Z= 0.358
  Chirality :  0.037   0.162   1902
  Planarity :  0.004   0.045   1240
  Dihedral  : 31.567 177.695   3513
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 17.64 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.29), residues: 711
  helix:  1.39 (0.21), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.18 (0.42), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.002   HIS G  79 
 PHE   0.018   0.002   PHE G  60 
 TYR   0.011   0.001   TYR E 102 
 ARG   0.008   0.000   ARG D  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03860 (  707)
  hydrogen bonds       : angle       3.24972 ( 1794)
  covalent geometry    : bond        0.00433 (11542)
  covalent geometry    : angle       0.61133 (16637)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
REVERT: D  119 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8169 (tmmt)
REVERT: F   31 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.8039 (mmm160)
REVERT: F   51 ARG cc_start: 0.8196 (mtt180) cc_final: 0.7900 (mtt-85)
REVERT: F   87 LYS cc_start: 0.8830 (ttpt) cc_final: 0.8529 (ttmt)
REVERT: H   84 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7693 (mmtt)
REVERT: H  104 GLU cc_start: 0.7601 (tp30) cc_final: 0.7372 (tp30)
REVERT: C   62 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7410 (mm-30)
REVERT: C   96 ASN cc_start: 0.7932 (p0) cc_final: 0.7729 (p0)
REVERT: C  101 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7781 (mt-10)
REVERT: G   81 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8336 (tp)
  outliers start: 19
  outliers final: 12
  residues processed: 115
  average time/residue: 0.3071
  time to fit residues: 46.4893
Evaluate side-chains
  105 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   82 THR
Chi-restraints excluded: chain G residue   81 LEU
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue  104 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 84 optimal weight:   10.0000
   chunk 35 optimal weight:    3.9990
   chunk 81 optimal weight:   10.0000
   chunk 65 optimal weight:    0.0060
   chunk 75 optimal weight:   10.0000
   overall best weight:    1.8004

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  44 GLN
C  79 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.181073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.124771 restraints weight = 14997.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.125588 restraints weight = 10166.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.126161 restraints weight = 9315.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11542  Z= 0.193
  Angle     :  0.609  13.311  16637  Z= 0.352
  Chirality :  0.037   0.186   1902
  Planarity :  0.004   0.047   1240
  Dihedral  : 31.456 177.351   3513
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 17.15 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.24 (0.29), residues: 711
  helix:  1.55 (0.21), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.19 (0.41), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS G  79 
 PHE   0.019   0.002   PHE G  60 
 TYR   0.012   0.001   TYR E 102 
 ARG   0.004   0.000   ARG F  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03786 (  707)
  hydrogen bonds       : angle       3.22468 ( 1794)
  covalent geometry    : bond        0.00445 (11542)
  covalent geometry    : angle       0.60891 (16637)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ASP cc_start: 0.7003 (t0) cc_final: 0.6783 (t0)
REVERT: D   86 ASN cc_start: 0.7627 (m-40) cc_final: 0.7200 (m-40)
REVERT: D  119 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8121 (tmmt)
REVERT: F   51 ARG cc_start: 0.8178 (mtt180) cc_final: 0.7930 (mtt-85)
REVERT: F   87 LYS cc_start: 0.8844 (ttpt) cc_final: 0.8538 (ttmt)
REVERT: H   84 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7737 (mmtt)
REVERT: C   62 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7364 (mm-30)
REVERT: C  101 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7759 (mt-10)
  outliers start: 22
  outliers final: 17
  residues processed: 113
  average time/residue: 0.2793
  time to fit residues: 42.3961
Evaluate side-chains
  108 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  121 THR
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   82 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Chi-restraints excluded: chain G residue   98 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 87 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0870
   chunk 10 optimal weight:    0.3980
   chunk 65 optimal weight:    6.9990
   chunk 83 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0770
   overall best weight:    0.8718

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 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 = 0.4219 r_free = 0.4219 target = 0.183403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.128295 restraints weight = 15072.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.129562 restraints weight = 10070.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.130004 restraints weight = 9397.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11542  Z= 0.158
  Angle     :  0.573   9.409  16637  Z= 0.337
  Chirality :  0.035   0.140   1902
  Planarity :  0.004   0.046   1240
  Dihedral  : 31.135 178.032   3513
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 19.26 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.30), residues: 711
  helix:  1.93 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.22 (0.39), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS G  79 
 PHE   0.012   0.002   PHE G  60 
 TYR   0.015   0.001   TYR E  55 
 ARG   0.006   0.000   ARG B  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03592 (  707)
  hydrogen bonds       : angle       3.09903 ( 1794)
  covalent geometry    : bond        0.00352 (11542)
  covalent geometry    : angle       0.57334 (16637)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.790 
Fit side-chains
REVERT: D   86 ASN cc_start: 0.7644 (m-40) cc_final: 0.7250 (m-40)
REVERT: F   22 LEU cc_start: 0.7848 (mt) cc_final: 0.7515 (mt)
REVERT: F   51 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7922 (mtt-85)
REVERT: H  104 GLU cc_start: 0.7539 (tp30) cc_final: 0.7014 (tp30)
REVERT: H  107 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7556 (ttp80)
REVERT: C   62 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7487 (mm-30)
  outliers start: 15
  outliers final: 10
  residues processed: 103
  average time/residue: 0.2738
  time to fit residues: 37.9351
Evaluate side-chains
  95 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 89 optimal weight:   10.0000
   chunk 78 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   chunk 39 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 80 optimal weight:   20.0000
   chunk 86 optimal weight:    8.9990
   overall best weight:    3.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  44 GLN
C  96 ASN
G  54 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.177617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.121082 restraints weight = 15131.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.121612 restraints weight = 10640.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.122318 restraints weight = 9682.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.077  11542  Z= 0.302
  Angle     :  0.672  11.874  16637  Z= 0.381
  Chirality :  0.040   0.202   1902
  Planarity :  0.005   0.045   1240
  Dihedral  : 31.541 176.812   3513
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.42 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.29), residues: 711
  helix:  1.26 (0.21), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.25 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS B  71 
 PHE   0.033   0.003   PHE B  96 
 TYR   0.019   0.002   TYR F  84 
 ARG   0.006   0.001   ARG B  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04348 (  707)
  hydrogen bonds       : angle       3.41794 ( 1794)
  covalent geometry    : bond        0.00714 (11542)
  covalent geometry    : angle       0.67176 (16637)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.911 
Fit side-chains
REVERT: D   78 ASN cc_start: 0.8836 (t0) cc_final: 0.8289 (t0)
REVERT: D   82 ILE cc_start: 0.9109 (mt) cc_final: 0.8689 (mt)
REVERT: D  119 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8372 (ttmt)
REVERT: H  104 GLU cc_start: 0.7684 (tp30) cc_final: 0.7476 (tp30)
REVERT: C  101 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7788 (mt-10)
  outliers start: 21
  outliers final: 15
  residues processed: 110
  average time/residue: 0.2891
  time to fit residues: 42.5411
Evaluate side-chains
  104 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue  121 THR
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain F residue   44 SER
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   82 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 89 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 29 optimal weight:    1.9990
   chunk 84 optimal weight:   10.0000
   chunk 60 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 82 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 80 optimal weight:   20.0000
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  89 GLN
C  96 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4188 r_free = 0.4188 target = 0.180576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.124219 restraints weight = 15215.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.125730 restraints weight = 9908.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.126190 restraints weight = 9105.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11542  Z= 0.187
  Angle     :  0.595  10.591  16637  Z= 0.346
  Chirality :  0.036   0.145   1902
  Planarity :  0.005   0.073   1240
  Dihedral  : 31.179 178.856   3513
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 20.23 %
    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:  1.28 (0.29), residues: 711
  helix:  1.57 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.16 (0.39), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS G  79 
 PHE   0.018   0.002   PHE B  96 
 TYR   0.016   0.002   TYR F  84 
 ARG   0.011   0.001   ARG B  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03741 (  707)
  hydrogen bonds       : angle       3.22811 ( 1794)
  covalent geometry    : bond        0.00432 (11542)
  covalent geometry    : angle       0.59479 (16637)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.846 
Fit side-chains
  outliers start: 18
  outliers final: 14
  residues processed: 106
  average time/residue: 0.3033
  time to fit residues: 42.6649
Evaluate side-chains
  103 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue  121 THR
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   82 THR
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0980
   chunk 57 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0980
   chunk 43 optimal weight:    6.9990
   chunk 89 optimal weight:    9.9990
   chunk 35 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.182708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.127217 restraints weight = 15089.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.127888 restraints weight = 10351.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.128720 restraints weight = 9505.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11542  Z= 0.157
  Angle     :  0.573   9.966  16637  Z= 0.336
  Chirality :  0.035   0.144   1902
  Planarity :  0.004   0.044   1240
  Dihedral  : 31.001 178.702   3513
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 20.71 %
    Favored  : 76.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.30), residues: 711
  helix:  1.89 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.09 (0.39), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS G  79 
 PHE   0.012   0.002   PHE G  60 
 TYR   0.014   0.001   TYR F  84 
 ARG   0.006   0.000   ARG E 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03575 (  707)
  hydrogen bonds       : angle       3.12943 ( 1794)
  covalent geometry    : bond        0.00350 (11542)
  covalent geometry    : angle       0.57276 (16637)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.818 
Fit side-chains
REVERT: A   93 GLU cc_start: 0.8029 (tp30) cc_final: 0.7707 (tp30)
REVERT: B   31 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7720 (mtp-110)
REVERT: B   35 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7771 (mtt90)
REVERT: D   86 ASN cc_start: 0.7655 (m-40) cc_final: 0.7218 (m-40)
REVERT: D  108 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8439 (mp)
REVERT: F   22 LEU cc_start: 0.8040 (mt) cc_final: 0.7684 (mt)
REVERT: H  104 GLU cc_start: 0.7517 (tp30) cc_final: 0.7255 (tp30)
  outliers start: 19
  outliers final: 11
  residues processed: 108
  average time/residue: 0.2890
  time to fit residues: 41.9683
Evaluate side-chains
  102 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue  108 LEU
Chi-restraints excluded: chain E residue   47 VAL
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 86 optimal weight:    8.9990
   chunk 89 optimal weight:   10.0000
   chunk 44 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.178615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.121834 restraints weight = 15069.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.122688 restraints weight = 10339.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.123303 restraints weight = 9286.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11542  Z= 0.168
  Angle     :  0.574   9.705  16637  Z= 0.336
  Chirality :  0.035   0.146   1902
  Planarity :  0.004   0.043   1240
  Dihedral  : 30.976 178.360   3513
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 20.87 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.30), residues: 711
  helix:  1.92 (0.21), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.04 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS G  79 
 PHE   0.013   0.002   PHE G  60 
 TYR   0.013   0.001   TYR F  68 
 ARG   0.004   0.000   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03641 (  707)
  hydrogen bonds       : angle       3.11428 ( 1794)
  covalent geometry    : bond        0.00381 (11542)
  covalent geometry    : angle       0.57419 (16637)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A   93 GLU cc_start: 0.8058 (tp30) cc_final: 0.7724 (tp30)
REVERT: B   35 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7963 (ttm170)
REVERT: D   86 ASN cc_start: 0.7702 (m-40) cc_final: 0.7294 (m-40)
REVERT: D  108 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8409 (mp)
REVERT: D  119 LYS cc_start: 0.8555 (ttmt) cc_final: 0.8224 (tttp)
REVERT: F   22 LEU cc_start: 0.8108 (mt) cc_final: 0.7790 (mt)
REVERT: H  104 GLU cc_start: 0.7609 (tp30) cc_final: 0.7381 (tp30)
REVERT: H  107 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7556 (tmm-80)
  outliers start: 16
  outliers final: 10
  residues processed: 104
  average time/residue: 0.3069
  time to fit residues: 42.3940
Evaluate side-chains
  99 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain D residue  108 LEU
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 72 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 68 optimal weight:   20.0000
   chunk 49 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0670
   chunk 34 optimal weight:    0.9980
   overall best weight:    1.1922

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  48 GLN
C  96 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.179248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.120932 restraints weight = 15050.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.122283 restraints weight = 10680.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.122619 restraints weight = 9399.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.3636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11542  Z= 0.165
  Angle     :  0.572   9.402  16637  Z= 0.335
  Chirality :  0.035   0.138   1902
  Planarity :  0.004   0.042   1240
  Dihedral  : 30.883 178.445   3513
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.87 %
    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:  1.79 (0.30), residues: 711
  helix:  1.96 (0.22), residues: 520
  sheet:  None (None), residues: 0
  loop : -0.99 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS G  79 
 PHE   0.015   0.002   PHE G  60 
 TYR   0.012   0.001   TYR E  55 
 ARG   0.004   0.000   ARG F  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03617 (  707)
  hydrogen bonds       : angle       3.09910 ( 1794)
  covalent geometry    : bond        0.00371 (11542)
  covalent geometry    : angle       0.57240 (16637)

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

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

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1422 Ramachandran restraints generated.
    711 Oldfield, 0 Emsley, 711 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 1.785 
Fit side-chains
REVERT: A   93 GLU cc_start: 0.8052 (tp30) cc_final: 0.7719 (tp30)
REVERT: B   31 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7866 (mtp-110)
REVERT: B   35 ARG cc_start: 0.8077 (mtt90) cc_final: 0.7786 (mtt90)
REVERT: D   43 ILE cc_start: 0.6670 (mm) cc_final: 0.6386 (mt)
REVERT: D   86 ASN cc_start: 0.7685 (m-40) cc_final: 0.7274 (m-40)
REVERT: D  108 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8425 (mp)
REVERT: D  119 LYS cc_start: 0.8546 (ttmt) cc_final: 0.8226 (tttp)
REVERT: H  104 GLU cc_start: 0.7512 (tp30) cc_final: 0.7257 (tp30)
REVERT: H  107 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7484 (tmm-80)
  outliers start: 14
  outliers final: 11
  residues processed: 98
  average time/residue: 0.4346
  time to fit residues: 56.0316
Evaluate side-chains
  96 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 LEU
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   69 THR
Chi-restraints excluded: chain B residue   77 VAL
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue  108 LEU
Chi-restraints excluded: chain E residue  116 HIS
Chi-restraints excluded: chain H residue   54 SER
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain G residue   76 VAL
Chi-restraints excluded: chain G residue   82 THR
Chi-restraints excluded: chain G residue   89 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 88 optimal weight:   10.0000
   chunk 87 optimal weight:   10.0000
   chunk 52 optimal weight:    0.2980
   chunk 62 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   chunk 69 optimal weight:   10.0000
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  89 GLN
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  96 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.180185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.122608 restraints weight = 15118.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.123357 restraints weight = 10305.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.123775 restraints weight = 9150.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7568
moved from start:          0.3880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11542  Z= 0.150
  Angle     :  0.556   8.575  16637  Z= 0.329
  Chirality :  0.034   0.140   1902
  Planarity :  0.004   0.043   1240
  Dihedral  : 30.745 178.618   3513
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 21.52 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.06 (0.30), residues: 711
  helix:  2.14 (0.22), residues: 520
  sheet:  None (None), residues: 0
  loop : -0.85 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS G  79 
 PHE   0.013   0.002   PHE G  60 
 TYR   0.010   0.001   TYR E 102 
 ARG   0.004   0.000   ARG D  39 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03547 (  707)
  hydrogen bonds       : angle       3.03719 ( 1794)
  covalent geometry    : bond        0.00330 (11542)
  covalent geometry    : angle       0.55578 (16637)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3006.15 seconds
wall clock time: 54 minutes 20.85 seconds (3260.85 seconds total)