Starting phenix.real_space_refine
on Fri Feb 14 14:53:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7d69_30591/02_2025/7d69_30591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7d69_30591/02_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_30591/02_2025/7d69_30591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7d69_30591/02_2025/7d69_30591.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7d69_30591/02_2025/7d69_30591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7d69_30591/02_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.78, per 1000 atoms: 0.53
  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: 2.78
  Conformation dependent library (CDL) restraints added in 774.5 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: 5.57
  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: 4.15

  Time building geometry restraints manager: 3.26 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:             0.160
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     29.850
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.680
-------------------------------------------------------------------------------
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= 0.528
  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 

*********************** 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  : 0.894 
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: 0.3631
  time to fit residues: 57.5508
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  : 0.842 
-------------------------------------------------------------------------------
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 = 0.125447 restraints weight = 14638.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.126925 restraints weight = 9779.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.127209 restraints weight = 9369.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
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= 0.219
  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 

*********************** 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  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 LYS cc_start: 0.8001 (mttp) cc_final: 0.7797 (mttp)
REVERT: B   35 ARG cc_start: 0.7798 (mtt-85) cc_final: 0.7541 (mtt90)
REVERT: F   31 ARG cc_start: 0.8317 (mmm-85) cc_final: 0.8027 (mmm160)
REVERT: F   51 ARG cc_start: 0.8182 (mtt180) cc_final: 0.7909 (mtt-85)
REVERT: F   87 LYS cc_start: 0.8852 (ttpt) cc_final: 0.8530 (ttmt)
REVERT: H   41 GLU cc_start: 0.8335 (tm-30) cc_final: 0.8080 (tm-30)
REVERT: H   84 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7786 (mmtt)
REVERT: H   98 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8391 (ttmm)
REVERT: C  101 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7811 (mt-10)
REVERT: G   62 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7362 (mm-30)
  outliers start: 10
  outliers final: 3
  residues processed: 120
  average time/residue: 0.2942
  time to fit residues: 46.7429
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  : 0.951 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 58 optimal weight:    6.9990
   chunk 88 optimal weight:   10.0000
   chunk 37 optimal weight:    0.5980
   chunk 85 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    2.6986

-------------------------------------------------------------------------------
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  30 HIS
C  79 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.178539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.122094 restraints weight = 15044.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.122506 restraints weight = 11116.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.123648 restraints weight = 9961.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  11542  Z= 0.336
  Angle     :  0.651   7.764  16637  Z= 0.375
  Chirality :  0.039   0.174   1902
  Planarity :  0.005   0.048   1240
  Dihedral  : 31.814 176.589   3513
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 17.80 %
    Favored  : 78.64 %
  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:  0.63 (0.29), residues: 711
  helix:  1.07 (0.21), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.35 (0.42), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS G  79 
 PHE   0.018   0.002   PHE G  60 
 TYR   0.014   0.002   TYR E 102 
 ARG   0.008   0.001   ARG D  39 

*********************** 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
  127 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   78 ASN cc_start: 0.8815 (t0) cc_final: 0.8256 (t0)
REVERT: D   82 ILE cc_start: 0.9091 (mt) cc_final: 0.8659 (mt)
REVERT: D  119 LYS cc_start: 0.8708 (ttmt) cc_final: 0.8187 (tmmt)
REVERT: F   87 LYS cc_start: 0.8859 (ttpt) cc_final: 0.8524 (ttmt)
REVERT: H   84 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7770 (mmtt)
REVERT: H  104 GLU cc_start: 0.7613 (tp30) cc_final: 0.7387 (tp30)
REVERT: C   62 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7426 (mm-30)
REVERT: C   89 GLU cc_start: 0.7069 (mp0) cc_final: 0.6802 (pm20)
REVERT: C  101 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7820 (mt-10)
  outliers start: 22
  outliers final: 15
  residues processed: 118
  average time/residue: 0.3060
  time to fit residues: 47.8159
Evaluate side-chains
  106 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain A residue   81 SER
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
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:    5.9990
   chunk 31 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 84 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 81 optimal weight:   10.0000
   chunk 65 optimal weight:    0.5980
   chunk 75 optimal weight:   10.0000
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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
** 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 = 0.4213 r_free = 0.4213 target = 0.182764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.126697 restraints weight = 15003.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.127943 restraints weight = 10221.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.128464 restraints weight = 9405.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  11542  Z= 0.201
  Angle     :  0.596  13.280  16637  Z= 0.347
  Chirality :  0.036   0.169   1902
  Planarity :  0.004   0.045   1240
  Dihedral  : 31.325 177.924   3513
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 19.09 %
    Favored  : 78.64 %
  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:  1.32 (0.29), residues: 711
  helix:  1.62 (0.21), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.21 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS G  79 
 PHE   0.018   0.002   PHE G  60 
 TYR   0.011   0.001   TYR F  84 
 ARG   0.008   0.000   ARG D  39 

*********************** 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
  112 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
REVERT: D   86 ASN cc_start: 0.7467 (m-40) cc_final: 0.7056 (m-40)
REVERT: F   87 LYS cc_start: 0.8828 (ttpt) cc_final: 0.8497 (ttmt)
REVERT: H   41 GLU cc_start: 0.8209 (tm-30) cc_final: 0.7979 (tm-30)
REVERT: H   84 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7621 (mmtt)
REVERT: C   62 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7408 (mm-30)
REVERT: C  101 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7706 (mt-10)
  outliers start: 14
  outliers final: 9
  residues processed: 105
  average time/residue: 0.3015
  time to fit residues: 41.9594
Evaluate side-chains
  99 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain B residue   89 GLN
Chi-restraints excluded: chain D residue   29 THR
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   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:    0.6980
   chunk 87 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 = 0.4191 r_free = 0.4191 target = 0.180848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.124198 restraints weight = 15052.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.126211 restraints weight = 9890.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.126357 restraints weight = 8797.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  11542  Z= 0.248
  Angle     :  0.595   9.447  16637  Z= 0.347
  Chirality :  0.036   0.156   1902
  Planarity :  0.004   0.045   1240
  Dihedral  : 31.383 177.191   3513
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 20.06 %
    Favored  : 77.02 %
  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:  1.36 (0.29), residues: 711
  helix:  1.65 (0.21), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.21 (0.40), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS G  79 
 PHE   0.017   0.002   PHE G  60 
 TYR   0.016   0.002   TYR E  55 
 ARG   0.007   0.000   ARG D  39 

*********************** 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
  109 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.814 
Fit side-chains
REVERT: D   86 ASN cc_start: 0.7613 (m-40) cc_final: 0.7170 (m-40)
REVERT: F   87 LYS cc_start: 0.8838 (ttpt) cc_final: 0.8506 (ttmt)
REVERT: H   84 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7678 (mmtt)
REVERT: C   62 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7419 (mm-30)
REVERT: C  101 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7746 (mt-10)
  outliers start: 18
  outliers final: 13
  residues processed: 104
  average time/residue: 0.3073
  time to fit residues: 42.3945
Evaluate side-chains
  99 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
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   29 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 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=3.00
-------------------------------------------------------------------------------
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:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 51 optimal weight:    0.1980
   chunk 74 optimal weight:   10.0000
   chunk 39 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 80 optimal weight:   20.0000
   chunk 86 optimal weight:    8.9990
   overall best weight:    2.9784

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.178393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.121748 restraints weight = 15095.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.122415 restraints weight = 10537.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.123049 restraints weight = 9718.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  11542  Z= 0.351
  Angle     :  0.640  11.698  16637  Z= 0.367
  Chirality :  0.039   0.181   1902
  Planarity :  0.005   0.044   1240
  Dihedral  : 31.515 177.382   3513
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.26 %
    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:  0.97 (0.29), residues: 711
  helix:  1.32 (0.21), residues: 524
  sheet:  None (None), residues: 0
  loop : -1.24 (0.40), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS G  79 
 PHE   0.014   0.002   PHE G  60 
 TYR   0.016   0.002   TYR E  55 
 ARG   0.007   0.001   ARG D  39 

*********************** 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
  118 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.804 
Fit side-chains
REVERT: D   78 ASN cc_start: 0.8792 (t0) cc_final: 0.8247 (t0)
REVERT: D   82 ILE cc_start: 0.9123 (mt) cc_final: 0.8681 (mt)
REVERT: D  119 LYS cc_start: 0.8618 (ttmt) cc_final: 0.8303 (tttp)
REVERT: F   87 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8555 (ttmt)
REVERT: H  104 GLU cc_start: 0.7715 (tp30) cc_final: 0.7476 (tp30)
REVERT: H  107 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7595 (tmm-80)
REVERT: C  101 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7752 (mt-10)
  outliers start: 24
  outliers final: 17
  residues processed: 111
  average time/residue: 0.2916
  time to fit residues: 43.4610
Evaluate side-chains
  105 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
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   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   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
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:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 29 optimal weight:    0.8980
   chunk 84 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 82 optimal weight:   10.0000
   chunk 36 optimal weight:    0.9990
   chunk 80 optimal weight:   20.0000
   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**
B  89 GLN
** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  48 GLN
C  96 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.182192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.125537 restraints weight = 15234.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.126456 restraints weight = 10639.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.126986 restraints weight = 9472.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.3278

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= 0.190
  Angle     :  0.575  10.246  16637  Z= 0.337
  Chirality :  0.035   0.145   1902
  Planarity :  0.004   0.044   1240
  Dihedral  : 31.042 179.191   3513
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 21.20 %
    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:  1.55 (0.30), residues: 711
  helix:  1.79 (0.21), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.12 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS G  79 
 PHE   0.014   0.002   PHE G  60 
 TYR   0.016   0.001   TYR E  55 
 ARG   0.007   0.000   ARG F  51 

*********************** 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
  106 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.886 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7723 (ptmm)
REVERT: D   86 ASN cc_start: 0.7602 (m-40) cc_final: 0.7163 (m-40)
REVERT: D  108 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8381 (mp)
REVERT: D  119 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8231 (tttp)
REVERT: F   87 LYS cc_start: 0.8822 (ttpt) cc_final: 0.8522 (ttmt)
  outliers start: 16
  outliers final: 9
  residues processed: 101
  average time/residue: 0.2669
  time to fit residues: 36.7331
Evaluate side-chains
  94 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LYS
Chi-restraints excluded: chain B residue   46 ILE
Chi-restraints excluded: chain B residue   69 THR
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   82 THR
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:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 51 optimal weight:    0.0980
   chunk 57 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 67 optimal weight:    0.3980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 ** 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 = 0.4225 r_free = 0.4225 target = 0.183876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.128764 restraints weight = 15179.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.128837 restraints weight = 10666.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.129817 restraints weight = 10647.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11542  Z= 0.187
  Angle     :  0.564   9.992  16637  Z= 0.332
  Chirality :  0.035   0.134   1902
  Planarity :  0.004   0.043   1240
  Dihedral  : 30.924 178.823   3513
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 21.68 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.84 (0.30), residues: 711
  helix:  2.01 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.03 (0.39), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS G  79 
 PHE   0.036   0.002   PHE B  96 
 TYR   0.020   0.002   TYR F  84 
 ARG   0.008   0.000   ARG F  51 

*********************** 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
  107 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.807 
Fit side-chains
REVERT: D   86 ASN cc_start: 0.7628 (m-40) cc_final: 0.7219 (m-40)
REVERT: D  108 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8413 (mp)
REVERT: F   87 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8508 (ttmt)
REVERT: H  104 GLU cc_start: 0.7637 (tp30) cc_final: 0.7348 (tp30)
REVERT: H  107 ARG cc_start: 0.7922 (ttp80) cc_final: 0.7501 (tmm-80)
  outliers start: 16
  outliers final: 6
  residues processed: 101
  average time/residue: 0.2835
  time to fit residues: 38.8085
Evaluate side-chains
  91 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ILE
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 G residue   76 VAL
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:    0.4980
   chunk 13 optimal weight:    2.9990
   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:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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
** 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 = 0.4187 r_free = 0.4187 target = 0.180834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.123070 restraints weight = 15103.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.124753 restraints weight = 10314.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.124934 restraints weight = 9230.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.3777

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= 0.189
  Angle     :  0.563   9.927  16637  Z= 0.330
  Chirality :  0.035   0.138   1902
  Planarity :  0.004   0.043   1240
  Dihedral  : 30.804 178.678   3513
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.01 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.97 (0.30), residues: 711
  helix:  2.11 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -0.98 (0.39), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS G  79 
 PHE   0.022   0.002   PHE B  96 
 TYR   0.009   0.001   TYR F  68 
 ARG   0.009   0.000   ARG F  51 

*********************** 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
  102 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.874 
Fit side-chains
REVERT: A   93 GLU cc_start: 0.7971 (tp30) cc_final: 0.7659 (tp30)
REVERT: D   86 ASN cc_start: 0.7723 (m-40) cc_final: 0.7337 (m-40)
REVERT: D  108 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8462 (mp)
REVERT: D  119 LYS cc_start: 0.8494 (ttmt) cc_final: 0.8166 (tttp)
REVERT: F   87 LYS cc_start: 0.8831 (ttpt) cc_final: 0.8593 (ttpp)
REVERT: H  104 GLU cc_start: 0.7658 (tp30) cc_final: 0.7217 (tp30)
REVERT: H  107 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7550 (ttp80)
  outliers start: 14
  outliers final: 10
  residues processed: 99
  average time/residue: 0.2936
  time to fit residues: 39.1971
Evaluate side-chains
  94 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
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   89 GLN
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  108 LEU
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 G residue   76 VAL
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:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 72 optimal weight:    8.9990
   chunk 30 optimal weight:    2.9990
   chunk 82 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 68 optimal weight:   20.0000
   chunk 49 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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  56 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 = 0.4191 r_free = 0.4191 target = 0.180930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.123620 restraints weight = 15096.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.124902 restraints weight = 10339.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.125208 restraints weight = 9394.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.3856

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= 0.200
  Angle     :  0.560   9.782  16637  Z= 0.329
  Chirality :  0.035   0.136   1902
  Planarity :  0.004   0.043   1240
  Dihedral  : 30.749 178.533   3513
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 22.49 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.96 (0.30), residues: 711
  helix:  2.08 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -0.90 (0.39), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS G  79 
 PHE   0.020   0.002   PHE B  96 
 TYR   0.015   0.001   TYR F  84 
 ARG   0.009   0.000   ARG F  51 

********************** 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  : 0.840 
Fit side-chains
REVERT: A   93 GLU cc_start: 0.7972 (tp30) cc_final: 0.7658 (tp30)
REVERT: D   86 ASN cc_start: 0.7730 (m-40) cc_final: 0.7358 (m-40)
REVERT: D  108 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8435 (mp)
REVERT: D  119 LYS cc_start: 0.8484 (ttmt) cc_final: 0.8239 (ttmt)
REVERT: E  127 MET cc_start: 0.8635 (ttt) cc_final: 0.8257 (ttt)
REVERT: F   87 LYS cc_start: 0.8861 (ttpt) cc_final: 0.8631 (ttpp)
REVERT: H  104 GLU cc_start: 0.7550 (tp30) cc_final: 0.7097 (tp30)
REVERT: H  107 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7532 (ttp80)
  outliers start: 14
  outliers final: 10
  residues processed: 98
  average time/residue: 0.2820
  time to fit residues: 37.5217
Evaluate side-chains
  94 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
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   89 GLN
Chi-restraints excluded: chain D residue   29 THR
Chi-restraints excluded: chain D residue  108 LEU
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 G residue   76 VAL
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:    0.0870
   chunk 62 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 27 optimal weight:    0.3980
   chunk 69 optimal weight:   10.0000
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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
** 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 = 0.4193 r_free = 0.4193 target = 0.181569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.124656 restraints weight = 15169.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.125749 restraints weight = 10659.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.126143 restraints weight = 9535.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.4030

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= 0.179
  Angle     :  0.556   9.250  16637  Z= 0.327
  Chirality :  0.034   0.134   1902
  Planarity :  0.004   0.042   1240
  Dihedral  : 30.667 178.839   3513
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 23.30 %
    Favored  : 74.76 %
  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:  2.15 (0.30), residues: 711
  helix:  2.20 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -0.79 (0.39), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS G  79 
 PHE   0.021   0.002   PHE B  96 
 TYR   0.009   0.001   TYR E 102 
 ARG   0.009   0.000   ARG F  51 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2490.21 seconds
wall clock time: 45 minutes 45.07 seconds (2745.07 seconds total)