Starting phenix.real_space_refine
on Tue Jul 29 20:52:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6fq6_4298/07_2025/6fq6_4298.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6fq6_4298/07_2025/6fq6_4298.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6fq6_4298/07_2025/6fq6_4298.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6fq6_4298/07_2025/6fq6_4298.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6fq6_4298/07_2025/6fq6_4298.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6fq6_4298/07_2025/6fq6_4298.cif"
  }
  resolution = 4.0
  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=   0.003 sd=   0.027
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     294      5.49       5
     S      12      5.16       5
     C    6620      2.51       5
     N    2249      2.21       5
     O    2812      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11987
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
    Chain: "B"
      Number of atoms: 668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 668
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 832
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "E"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 4, 'TRANS': 91}
    Chain: "F"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 832
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 690
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
    Chain: "I"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Time building chain proxies: 7.33, per 1000 atoms: 0.61
  Number of scatterers: 11987
  At special positions: 0
  Unit cell: (77, 121.8, 112, 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      12     16.00
     P     294     15.00
     O    2812      8.00
     N    2249      7.00
     C    6620      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: 2.90
  Conformation dependent library (CDL) restraints added in 982.7 milliseconds
  

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1412

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      73.5% alpha, 2.4% beta
      147 base pairs and 260 stacking pairs defined.
    Time for finding SS restraints: 6.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 75
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.744A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 28
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 47 through 76
      removed outlier: 3.940A  pdb=" N   TYR B  51 " --> pdb=" O   SER B  47 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   GLU B  52 " --> pdb=" O   GLY B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.802A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 36
      removed outlier: 3.596A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.492A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.684A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.754A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 120
      removed outlier: 3.691A  pdb=" N   ALA D 104 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.685A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 28
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 47 through 76
      removed outlier: 4.048A  pdb=" N   TYR F  51 " --> pdb=" O   SER F  47 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   GLU F  52 " --> pdb=" O   GLY F  48 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.708A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.426A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
      removed outlier: 3.872A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
      removed outlier: 3.511A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
      removed outlier: 3.567A  pdb=" N   ALA H 104 " --> pdb=" O   PRO H 100 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.515A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.551A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.727A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.915A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.823A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.634A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 6.657A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    395 hydrogen bonds defined for protein.
    1167 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      376 hydrogen bonds
      744 hydrogen bond angles
      0 basepair planarities
      147 basepair parallelities
      260 stacking parallelities
  Total time for adding SS restraints: 4.54

  Time building geometry restraints manager: 3.24 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1413
        1.32 -     1.44: 4792
        1.44 -     1.56: 5985
        1.56 -     1.68: 588
        1.68 -     1.80: 22
  Bond restraints: 12800
  Sorted by residual:
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.496 -0.074 3.00e-02 1.11e+03 6.07e+00
  bond pdb=" C3'  DC I  52 "
       pdb=" O3'  DC I  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.492 -0.070 3.00e-02 1.11e+03 5.50e+00
  bond pdb=" C3'  DT I -59 "
       pdb=" O3'  DT I -59 "
    ideal  model  delta    sigma   weight residual
    1.422  1.491 -0.069 3.00e-02 1.11e+03 5.32e+00
  bond pdb=" C3'  DG J  52 "
       pdb=" O3'  DG J  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.488 -0.066 3.00e-02 1.11e+03 4.78e+00
  bond pdb=" C2   DC I  61 "
       pdb=" O2   DC I  61 "
    ideal  model  delta    sigma   weight residual
    1.237  1.196  0.041 2.00e-02 2.50e+03 4.22e+00
  ... (remaining 12795 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 17353
        2.13 -     4.26: 1079
        4.26 -     6.40: 105
        6.40 -     8.53: 14
        8.53 -    10.66: 4
  Bond angle restraints: 18555
  Sorted by residual:
  angle pdb=" C3'  DG I  20 "
        pdb=" O3'  DG I  20 "
        pdb=" P    DG I  21 "
      ideal   model   delta    sigma   weight residual
     120.20  127.48   -7.28 1.50e+00 4.44e-01 2.35e+01
  angle pdb=" O4'  DC I -26 "
        pdb=" C1'  DC I -26 "
        pdb=" N1   DC I -26 "
      ideal   model   delta    sigma   weight residual
     108.40  101.87    6.53 1.50e+00 4.44e-01 1.90e+01
  angle pdb=" O4'  DG I   4 "
        pdb=" C1'  DG I   4 "
        pdb=" N9   DG I   4 "
      ideal   model   delta    sigma   weight residual
     108.40  114.63   -6.23 1.50e+00 4.44e-01 1.72e+01
  angle pdb=" O4'  DC I -28 "
        pdb=" C1'  DC I -28 "
        pdb=" N1   DC I -28 "
      ideal   model   delta    sigma   weight residual
     108.40  102.36    6.04 1.50e+00 4.44e-01 1.62e+01
  angle pdb=" C3'  DT I -59 "
        pdb=" O3'  DT I -59 "
        pdb=" P    DC I -58 "
      ideal   model   delta    sigma   weight residual
     120.20  126.24   -6.04 1.50e+00 4.44e-01 1.62e+01
  ... (remaining 18550 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.22: 5496
       32.22 -    64.45: 1400
       64.45 -    96.67: 36
       96.67 -   128.90: 4
      128.90 -   161.12: 2
  Dihedral angle restraints: 6938
    sinusoidal: 4752
      harmonic: 2186
  Sorted by residual:
  dihedral pdb=" C4'  DT I -59 "
           pdb=" C3'  DT I -59 "
           pdb=" O3'  DT I -59 "
           pdb=" P    DC I -58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   58.88  161.12     1      3.50e+01 8.16e-04 1.53e+01
  dihedral pdb=" C4'  DG I  20 "
           pdb=" C3'  DG I  20 "
           pdb=" O3'  DG I  20 "
           pdb=" P    DG I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   64.07  155.93     1      3.50e+01 8.16e-04 1.50e+01
  dihedral pdb=" C4'  DC I  52 "
           pdb=" C3'  DC I  52 "
           pdb=" O3'  DC I  52 "
           pdb=" P    DC I  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00  103.74  116.26     1      3.50e+01 8.16e-04 1.13e+01
  ... (remaining 6935 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 1771
       0.088 -    0.176: 322
       0.176 -    0.263: 24
       0.263 -    0.351: 2
       0.351 -    0.439: 1
  Chirality restraints: 2120
  Sorted by residual:
  chirality pdb=" C1'  DG I   4 "
            pdb=" O4'  DG I   4 "
            pdb=" C2'  DG I   4 "
            pdb=" N9   DG I   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    1.98    0.44 2.00e-01 2.50e+01 4.81e+00
  chirality pdb=" C1'  DG I  20 "
            pdb=" O4'  DG I  20 "
            pdb=" C2'  DG I  20 "
            pdb=" N9   DG I  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.11    0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" C1'  DG I -21 "
            pdb=" O4'  DG I -21 "
            pdb=" C2'  DG I -21 "
            pdb=" N9   DG I -21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.15    0.27 2.00e-01 2.50e+01 1.76e+00
  ... (remaining 2117 not shown)

  Planarity restraints: 1326
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  61 "    0.001 2.00e-02 2.50e+03   3.07e-02 2.12e+01
        pdb=" N1   DC I  61 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DC I  61 "   -0.071 2.00e-02 2.50e+03
        pdb=" O2   DC I  61 "    0.046 2.00e-02 2.50e+03
        pdb=" N3   DC I  61 "    0.008 2.00e-02 2.50e+03
        pdb=" C4   DC I  61 "   -0.025 2.00e-02 2.50e+03
        pdb=" N4   DC I  61 "    0.018 2.00e-02 2.50e+03
        pdb=" C5   DC I  61 "    0.008 2.00e-02 2.50e+03
        pdb=" C6   DC I  61 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I -28 "    0.065 2.00e-02 2.50e+03   3.01e-02 2.03e+01
        pdb=" N1   DC I -28 "   -0.040 2.00e-02 2.50e+03
        pdb=" C2   DC I -28 "   -0.013 2.00e-02 2.50e+03
        pdb=" O2   DC I -28 "   -0.010 2.00e-02 2.50e+03
        pdb=" N3   DC I -28 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DC I -28 "    0.005 2.00e-02 2.50e+03
        pdb=" N4   DC I -28 "    0.033 2.00e-02 2.50e+03
        pdb=" C5   DC I -28 "   -0.009 2.00e-02 2.50e+03
        pdb=" C6   DC I -28 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I -26 "    0.060 2.00e-02 2.50e+03   2.99e-02 2.01e+01
        pdb=" N1   DC I -26 "   -0.047 2.00e-02 2.50e+03
        pdb=" C2   DC I -26 "   -0.002 2.00e-02 2.50e+03
        pdb=" O2   DC I -26 "   -0.018 2.00e-02 2.50e+03
        pdb=" N3   DC I -26 "    0.000 2.00e-02 2.50e+03
        pdb=" C4   DC I -26 "    0.007 2.00e-02 2.50e+03
        pdb=" N4   DC I -26 "    0.032 2.00e-02 2.50e+03
        pdb=" C5   DC I -26 "   -0.029 2.00e-02 2.50e+03
        pdb=" C6   DC I -26 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1323 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2243
        2.79 -     3.32: 11197
        3.32 -     3.84: 25040
        3.84 -     4.37: 28236
        4.37 -     4.90: 39457
  Nonbonded interactions: 106173
  Sorted by model distance:
  nonbonded pdb=" OG  SER G  18 "
            pdb=" O   PHE G  25 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OG  SER C  18 "
            pdb=" O   PHE C  25 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   VAL H 108 "
            pdb=" OG1 THR H 112 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" NZ  LYS D  43 "
            pdb=" O   PRO D  47 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" O   VAL D 108 "
            pdb=" OG1 THR D 112 "
     model   vdw
     2.333 3.040
  ... (remaining 106168 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 20 through 101)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 33 through 121)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.360
  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:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     33.930
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
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   0.074  12800  Z= 0.383
  Angle     :  1.104  10.662  18555  Z= 0.656
  Chirality :  0.066   0.439   2120
  Planarity :  0.008   0.040   1326
  Dihedral  : 26.701 161.124   5526
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  1.44 %
    Favored  : 98.24 %
  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: -0.84 (0.27), residues: 736
  helix: -0.06 (0.20), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.57 (0.35), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.003   HIS C  82 
 PHE   0.021   0.004   PHE E  78 
 TYR   0.032   0.004   TYR A  54 
 ARG   0.005   0.001   ARG C  11 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13524 (  771)
  hydrogen bonds       : angle       5.78257 ( 1911)
  covalent geometry    : bond        0.00852 (12800)
  covalent geometry    : angle       1.10432 (18555)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 308
  time to evaluate  : 0.948 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 LEU cc_start: 0.6281 (mt) cc_final: 0.5838 (mt)
REVERT: A   93 GLN cc_start: 0.8110 (tt0) cc_final: 0.6481 (tt0)
REVERT: A  100 LEU cc_start: 0.9279 (mt) cc_final: 0.9033 (pp)
REVERT: A  120 MET cc_start: 0.7083 (mtp) cc_final: 0.6080 (mtp)
REVERT: A  124 ILE cc_start: 0.9470 (mt) cc_final: 0.8921 (mp)
REVERT: A  129 ARG cc_start: 0.9134 (mtp180) cc_final: 0.8642 (mmm160)
REVERT: B   59 LYS cc_start: 0.9096 (ttpt) cc_final: 0.8878 (tppt)
REVERT: B   70 VAL cc_start: 0.9337 (t) cc_final: 0.9073 (t)
REVERT: B   88 TYR cc_start: 0.8315 (m-10) cc_final: 0.7667 (m-80)
REVERT: B   96 THR cc_start: 0.8707 (m) cc_final: 0.8446 (p)
REVERT: C   61 GLU cc_start: 0.9202 (tp30) cc_final: 0.8889 (tm-30)
REVERT: C   84 GLN cc_start: 0.8066 (tp40) cc_final: 0.7165 (tp40)
REVERT: C   94 ASN cc_start: 0.8432 (t0) cc_final: 0.8117 (t0)
REVERT: C  113 SER cc_start: 0.8820 (m) cc_final: 0.8586 (p)
REVERT: D   34 TYR cc_start: 0.8699 (m-80) cc_final: 0.8435 (m-10)
REVERT: D   41 VAL cc_start: 0.9538 (t) cc_final: 0.9324 (t)
REVERT: D   51 ILE cc_start: 0.8376 (pt) cc_final: 0.8030 (tt)
REVERT: D   73 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8396 (tt0)
REVERT: E   82 LEU cc_start: 0.5668 (mt) cc_final: 0.5353 (mt)
REVERT: E   92 LEU cc_start: 0.9246 (mt) cc_final: 0.8990 (mt)
REVERT: E   93 GLN cc_start: 0.8743 (tt0) cc_final: 0.7597 (tp-100)
REVERT: E  106 ASP cc_start: 0.8654 (m-30) cc_final: 0.8345 (m-30)
REVERT: E  120 MET cc_start: 0.7320 (mtp) cc_final: 0.6917 (mtt)
REVERT: F   25 ASN cc_start: 0.5810 (m-40) cc_final: 0.5327 (m-40)
REVERT: F   44 LYS cc_start: 0.7914 (tttt) cc_final: 0.7452 (tmmt)
REVERT: F   70 VAL cc_start: 0.9311 (t) cc_final: 0.9063 (t)
REVERT: F   88 TYR cc_start: 0.8243 (m-10) cc_final: 0.7772 (m-10)
REVERT: G   35 ARG cc_start: 0.8699 (mtm180) cc_final: 0.8216 (mtp180)
REVERT: G   64 GLU cc_start: 0.9426 (tt0) cc_final: 0.9132 (tp30)
REVERT: G   94 ASN cc_start: 0.8753 (t0) cc_final: 0.8495 (t0)
REVERT: H   34 TYR cc_start: 0.8028 (m-80) cc_final: 0.7797 (m-10)
REVERT: H   37 TYR cc_start: 0.7736 (m-80) cc_final: 0.7450 (m-80)
REVERT: H   73 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8261 (tt0)
REVERT: H  106 HIS cc_start: 0.8454 (m-70) cc_final: 0.8090 (m90)
  outliers start: 2
  outliers final: 2
  residues processed: 310
  average time/residue: 0.3059
  time to fit residues: 124.8869
Evaluate side-chains
  167 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 165
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain H residue  113 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 75 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 50 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 77 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 47 optimal weight:    8.9990
   chunk 57 optimal weight:    8.9990
   chunk 89 optimal weight:   10.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A  68 GLN
** A  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 110 ASN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
F  25 ASN
F  27 GLN
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN
H  46 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.055233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.047848 restraints weight = 109796.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.049080 restraints weight = 67229.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.049939 restraints weight = 45896.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.3345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  12800  Z= 0.289
  Angle     :  0.762  10.311  18555  Z= 0.446
  Chirality :  0.042   0.165   2120
  Planarity :  0.006   0.040   1326
  Dihedral  : 31.746 174.160   4052
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 25.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 19.33 %
    Favored  : 76.84 %
  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:  0.21 (0.29), residues: 736
  helix:  0.75 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.43 (0.38), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.002   HIS D  79 
 PHE   0.018   0.003   PHE D  62 
 TYR   0.017   0.002   TYR G  50 
 ARG   0.012   0.001   ARG F  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08605 (  771)
  hydrogen bonds       : angle       4.38010 ( 1911)
  covalent geometry    : bond        0.00629 (12800)
  covalent geometry    : angle       0.76223 (18555)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 182
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8655 (mmt) cc_final: 0.8426 (mmm)
REVERT: A  120 MET cc_start: 0.7293 (mtp) cc_final: 0.6963 (mtp)
REVERT: B   59 LYS cc_start: 0.9536 (ttpt) cc_final: 0.9185 (tptp)
REVERT: B   63 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8366 (mt-10)
REVERT: B   88 TYR cc_start: 0.8638 (m-10) cc_final: 0.8038 (m-80)
REVERT: C   61 GLU cc_start: 0.9244 (tp30) cc_final: 0.8918 (tm-30)
REVERT: D   34 TYR cc_start: 0.8202 (m-80) cc_final: 0.7932 (m-80)
REVERT: D   73 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8784 (tp30)
REVERT: D  106 HIS cc_start: 0.8389 (m-70) cc_final: 0.7990 (m90)
REVERT: E   93 GLN cc_start: 0.8327 (tt0) cc_final: 0.7193 (tp40)
REVERT: E   97 GLU cc_start: 0.7699 (mt-10) cc_final: 0.6786 (mt-10)
REVERT: E  100 LEU cc_start: 0.9576 (mt) cc_final: 0.9354 (mm)
REVERT: F   25 ASN cc_start: 0.6259 (m110) cc_final: 0.5830 (m-40)
REVERT: F   44 LYS cc_start: 0.8118 (tttt) cc_final: 0.7664 (ttpt)
REVERT: F   59 LYS cc_start: 0.9436 (tptm) cc_final: 0.8958 (tppt)
REVERT: F   88 TYR cc_start: 0.8531 (m-10) cc_final: 0.8039 (m-10)
REVERT: G   64 GLU cc_start: 0.9241 (tt0) cc_final: 0.8750 (tp30)
REVERT: G   84 GLN cc_start: 0.8655 (tp40) cc_final: 0.8311 (tt0)
REVERT: H   39 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.8055 (m-80)
REVERT: H   73 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8679 (tp30)
REVERT: H  106 HIS cc_start: 0.8783 (m-70) cc_final: 0.8244 (m-70)
  outliers start: 24
  outliers final: 16
  residues processed: 192
  average time/residue: 0.2545
  time to fit residues: 68.4096
Evaluate side-chains
  151 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain E residue   55 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   51 TYR
Chi-restraints excluded: chain F residue   64 ASN
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   39 TYR
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 78 optimal weight:   10.0000
   chunk 8 optimal weight:    8.9990
   chunk 31 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9990
   chunk 75 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 95 optimal weight:    6.9990
   chunk 12 optimal weight:    8.9990
   chunk 90 optimal weight:   10.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  94 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.054542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.047729 restraints weight = 113742.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.048901 restraints weight = 70836.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.049709 restraints weight = 48544.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.4366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067  12800  Z= 0.275
  Angle     :  0.742  12.515  18555  Z= 0.436
  Chirality :  0.042   0.160   2120
  Planarity :  0.006   0.052   1326
  Dihedral  : 31.640 170.788   4048
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 25.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 20.29 %
    Favored  : 75.56 %
  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:  0.22 (0.29), residues: 736
  helix:  0.81 (0.21), residues: 535
  sheet:  None (None), residues: 0
  loop : -1.53 (0.38), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS F  75 
 PHE   0.026   0.003   PHE D  62 
 TYR   0.016   0.002   TYR D  37 
 ARG   0.012   0.001   ARG E 116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08084 (  771)
  hydrogen bonds       : angle       4.28403 ( 1911)
  covalent geometry    : bond        0.00595 (12800)
  covalent geometry    : angle       0.74239 (18555)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 1.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ILE cc_start: 0.7472 (mm) cc_final: 0.7202 (mm)
REVERT: A  103 LEU cc_start: 0.9355 (mt) cc_final: 0.9110 (mt)
REVERT: A  104 PHE cc_start: 0.8935 (m-80) cc_final: 0.8694 (m-80)
REVERT: B   25 ASN cc_start: 0.5537 (m110) cc_final: 0.5154 (m110)
REVERT: B   88 TYR cc_start: 0.8568 (m-10) cc_final: 0.8073 (m-80)
REVERT: C   61 GLU cc_start: 0.9217 (tp30) cc_final: 0.8832 (tm-30)
REVERT: D   73 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8740 (tp30)
REVERT: D  106 HIS cc_start: 0.8393 (m-70) cc_final: 0.7938 (m-70)
REVERT: F   25 ASN cc_start: 0.5906 (m110) cc_final: 0.5576 (m-40)
REVERT: F   59 LYS cc_start: 0.9570 (tptm) cc_final: 0.9152 (tppt)
REVERT: F   88 TYR cc_start: 0.8525 (m-10) cc_final: 0.8014 (m-10)
REVERT: G   64 GLU cc_start: 0.9101 (tt0) cc_final: 0.8605 (tp30)
REVERT: G   84 GLN cc_start: 0.8632 (tp40) cc_final: 0.8359 (tt0)
REVERT: G   94 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7824 (m110)
REVERT: H   73 GLU cc_start: 0.9163 (mm-30) cc_final: 0.8508 (tp30)
REVERT: H  106 HIS cc_start: 0.8815 (m-70) cc_final: 0.8364 (m170)
  outliers start: 26
  outliers final: 16
  residues processed: 171
  average time/residue: 0.2953
  time to fit residues: 73.9443
Evaluate side-chains
  144 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   64 ASN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   55 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   73 THR
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   94 ASN
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   87 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 59 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  94 ASN
H 106 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.053987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.047293 restraints weight = 113175.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.048451 restraints weight = 69791.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.049253 restraints weight = 47694.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.4921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071  12800  Z= 0.267
  Angle     :  0.733   9.534  18555  Z= 0.430
  Chirality :  0.041   0.158   2120
  Planarity :  0.005   0.057   1326
  Dihedral  : 31.750 169.409   4048
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 26.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 21.73 %
    Favored  : 73.96 %
  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:  0.21 (0.29), residues: 736
  helix:  0.79 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -1.50 (0.39), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS D  46 
 PHE   0.020   0.003   PHE D  62 
 TYR   0.014   0.002   TYR C  50 
 ARG   0.004   0.001   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08004 (  771)
  hydrogen bonds       : angle       4.22608 ( 1911)
  covalent geometry    : bond        0.00580 (12800)
  covalent geometry    : angle       0.73315 (18555)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 LEU cc_start: 0.9452 (mt) cc_final: 0.9219 (mt)
REVERT: B   25 ASN cc_start: 0.5631 (m110) cc_final: 0.5364 (m110)
REVERT: B   88 TYR cc_start: 0.8581 (m-10) cc_final: 0.8036 (m-80)
REVERT: C   61 GLU cc_start: 0.9155 (tp30) cc_final: 0.8862 (tm-30)
REVERT: D   73 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8748 (tp30)
REVERT: D  106 HIS cc_start: 0.8207 (m-70) cc_final: 0.7705 (m90)
REVERT: E   97 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7535 (mt-10)
REVERT: F   25 ASN cc_start: 0.5932 (m110) cc_final: 0.5583 (m-40)
REVERT: F   59 LYS cc_start: 0.9576 (tptm) cc_final: 0.9203 (tppt)
REVERT: F   88 TYR cc_start: 0.8499 (m-10) cc_final: 0.7983 (m-10)
REVERT: G   64 GLU cc_start: 0.9079 (tt0) cc_final: 0.8595 (tp30)
REVERT: G   84 GLN cc_start: 0.8648 (tp40) cc_final: 0.8368 (tt0)
REVERT: H   73 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8403 (tp30)
REVERT: H   77 LEU cc_start: 0.8987 (mm) cc_final: 0.8546 (mm)
REVERT: H  106 HIS cc_start: 0.8334 (m90) cc_final: 0.7867 (m90)
  outliers start: 27
  outliers final: 22
  residues processed: 158
  average time/residue: 0.3024
  time to fit residues: 70.8845
Evaluate side-chains
  146 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   64 ASN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue   97 LEU
Chi-restraints excluded: chain E residue   55 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   93 GLN
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   41 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 98 optimal weight:   10.0000
   chunk 90 optimal weight:   10.0000
   chunk 80 optimal weight:    6.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 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 = 0.3599 r_free = 0.3599 target = 0.055355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.048380 restraints weight = 113185.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.049552 restraints weight = 70068.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.050393 restraints weight = 48200.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.5188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  12800  Z= 0.213
  Angle     :  0.694   9.361  18555  Z= 0.407
  Chirality :  0.039   0.156   2120
  Planarity :  0.005   0.044   1326
  Dihedral  : 31.746 168.813   4048
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 22.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 22.36 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.30), residues: 736
  helix:  0.94 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -1.53 (0.39), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D  46 
 PHE   0.016   0.002   PHE D  62 
 TYR   0.013   0.002   TYR D  37 
 ARG   0.004   0.000   ARG C  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06499 (  771)
  hydrogen bonds       : angle       4.01365 ( 1911)
  covalent geometry    : bond        0.00460 (12800)
  covalent geometry    : angle       0.69416 (18555)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 145
  time to evaluate  : 1.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.5594 (m110) cc_final: 0.5347 (m110)
REVERT: B   88 TYR cc_start: 0.8572 (m-10) cc_final: 0.8046 (m-80)
REVERT: C   61 GLU cc_start: 0.9142 (tp30) cc_final: 0.8848 (tm-30)
REVERT: D   56 MET cc_start: 0.7277 (tpt) cc_final: 0.6712 (tpt)
REVERT: D   73 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8675 (tp30)
REVERT: D  106 HIS cc_start: 0.8069 (m-70) cc_final: 0.7576 (m90)
REVERT: F   25 ASN cc_start: 0.5895 (m110) cc_final: 0.5547 (m-40)
REVERT: F   59 LYS cc_start: 0.9571 (tptm) cc_final: 0.9125 (tppt)
REVERT: F   88 TYR cc_start: 0.8510 (m-10) cc_final: 0.8003 (m-10)
REVERT: G   64 GLU cc_start: 0.9037 (tt0) cc_final: 0.8529 (tp30)
REVERT: G   84 GLN cc_start: 0.8672 (tp40) cc_final: 0.8455 (tt0)
REVERT: H   73 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8452 (tp30)
REVERT: H  106 HIS cc_start: 0.8340 (m90) cc_final: 0.7943 (m-70)
  outliers start: 32
  outliers final: 23
  residues processed: 163
  average time/residue: 0.2864
  time to fit residues: 68.0719
Evaluate side-chains
  148 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   55 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   93 GLN
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  123 ASP
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   chunk 42 optimal weight:    7.9990
   chunk 76 optimal weight:   10.0000
   chunk 58 optimal weight:   20.0000
   chunk 61 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 60 optimal weight:    5.9990
   chunk 86 optimal weight:   10.0000
   chunk 28 optimal weight:    1.9990
   overall best weight:    6.3992

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

Flipped N/Q/H residues before XYZ refinement:
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 106 HIS
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  79 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.052451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.045613 restraints weight = 116463.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.046701 restraints weight = 72801.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.047463 restraints weight = 50208.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.5907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.088  12800  Z= 0.308
  Angle     :  0.773   9.528  18555  Z= 0.451
  Chirality :  0.044   0.407   2120
  Planarity :  0.006   0.051   1326
  Dihedral  : 32.076 167.456   4048
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 31.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 24.76 %
    Favored  : 69.81 %
  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: -0.16 (0.29), residues: 736
  helix:  0.51 (0.21), residues: 530
  sheet:  None (None), residues: 0
  loop : -1.57 (0.40), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS F  75 
 PHE   0.018   0.002   PHE D  62 
 TYR   0.017   0.002   TYR D  37 
 ARG   0.008   0.001   ARG G  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09730 (  771)
  hydrogen bonds       : angle       4.50200 ( 1911)
  covalent geometry    : bond        0.00664 (12800)
  covalent geometry    : angle       0.77271 (18555)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 1.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.6017 (m110) cc_final: 0.5706 (m110)
REVERT: B   88 TYR cc_start: 0.8619 (m-10) cc_final: 0.8014 (m-80)
REVERT: C   61 GLU cc_start: 0.9101 (tp30) cc_final: 0.8653 (tm-30)
REVERT: D   39 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.7765 (m-80)
REVERT: D   56 MET cc_start: 0.7349 (tpt) cc_final: 0.7145 (tpt)
REVERT: D   73 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8746 (tp30)
REVERT: D  106 HIS cc_start: 0.8130 (m90) cc_final: 0.7657 (m90)
REVERT: F   25 ASN cc_start: 0.5852 (m110) cc_final: 0.5470 (m-40)
REVERT: F   59 LYS cc_start: 0.9606 (tptm) cc_final: 0.9174 (tppt)
REVERT: F   88 TYR cc_start: 0.8449 (m-10) cc_final: 0.7832 (m-10)
REVERT: G   84 GLN cc_start: 0.8719 (tp40) cc_final: 0.8375 (tt0)
REVERT: H   39 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.7807 (m-80)
REVERT: H   73 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8274 (tp30)
  outliers start: 34
  outliers final: 27
  residues processed: 148
  average time/residue: 0.2716
  time to fit residues: 59.0905
Evaluate side-chains
  145 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   39 TYR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   93 GLN
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  123 ASP
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   26 ILE
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   39 TYR
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 61 optimal weight:    0.9980
   chunk 85 optimal weight:   10.0000
   chunk 83 optimal weight:   10.0000
   chunk 94 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 GLN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.054142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.047219 restraints weight = 113092.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.048343 restraints weight = 70686.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.049146 restraints weight = 48812.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.5981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  12800  Z= 0.228
  Angle     :  0.731  11.738  18555  Z= 0.423
  Chirality :  0.041   0.366   2120
  Planarity :  0.005   0.039   1326
  Dihedral  : 32.066 168.581   4048
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 23.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 27.64 %
    Favored  : 67.57 %
  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: -0.00 (0.30), residues: 736
  helix:  0.65 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -1.60 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.014   0.002   PHE D  62 
 TYR   0.014   0.002   TYR D  37 
 ARG   0.004   0.001   ARG E  63 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07014 (  771)
  hydrogen bonds       : angle       4.19187 ( 1911)
  covalent geometry    : bond        0.00495 (12800)
  covalent geometry    : angle       0.73087 (18555)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.5754 (m110) cc_final: 0.5421 (m110)
REVERT: B   88 TYR cc_start: 0.8609 (m-10) cc_final: 0.7961 (m-10)
REVERT: C   61 GLU cc_start: 0.9107 (tp30) cc_final: 0.8669 (tm-30)
REVERT: D   73 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8630 (tp30)
REVERT: D  106 HIS cc_start: 0.7903 (m90) cc_final: 0.7641 (m90)
REVERT: F   25 ASN cc_start: 0.5945 (m110) cc_final: 0.5602 (m-40)
REVERT: F   59 LYS cc_start: 0.9606 (tptm) cc_final: 0.9223 (tppt)
REVERT: F   88 TYR cc_start: 0.8537 (m-10) cc_final: 0.8033 (m-10)
REVERT: G   84 GLN cc_start: 0.8723 (tp40) cc_final: 0.8430 (tt0)
REVERT: H   73 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8391 (tp30)
REVERT: H  106 HIS cc_start: 0.8345 (m90) cc_final: 0.7939 (m170)
  outliers start: 30
  outliers final: 21
  residues processed: 146
  average time/residue: 0.2057
  time to fit residues: 44.6860
Evaluate side-chains
  137 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   93 GLN
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  123 ASP
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   26 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 4 optimal weight:   20.0000
   chunk 66 optimal weight:    6.9990
   chunk 67 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 19 optimal weight:    9.9990
   chunk 52 optimal weight:    6.9990
   chunk 53 optimal weight:   20.0000
   chunk 18 optimal weight:    8.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 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 = 0.3546 r_free = 0.3546 target = 0.052937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.046183 restraints weight = 115187.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.047259 restraints weight = 72223.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.048012 restraints weight = 49891.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.6303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077  12800  Z= 0.277
  Angle     :  0.757  12.348  18555  Z= 0.440
  Chirality :  0.042   0.334   2120
  Planarity :  0.005   0.047   1326
  Dihedral  : 32.179 167.491   4048
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 28.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 27.00 %
    Favored  : 68.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.29), residues: 736
  helix:  0.49 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -1.61 (0.40), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS F  75 
 PHE   0.015   0.002   PHE A  78 
 TYR   0.017   0.002   TYR D  37 
 ARG   0.008   0.001   ARG A  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08476 (  771)
  hydrogen bonds       : angle       4.38609 ( 1911)
  covalent geometry    : bond        0.00596 (12800)
  covalent geometry    : angle       0.75668 (18555)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 120
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.5882 (m110) cc_final: 0.5540 (m110)
REVERT: B   88 TYR cc_start: 0.8610 (m-10) cc_final: 0.7960 (m-10)
REVERT: C   61 GLU cc_start: 0.9071 (tp30) cc_final: 0.8631 (tm-30)
REVERT: D   56 MET cc_start: 0.7620 (tpt) cc_final: 0.7349 (tpt)
REVERT: D   73 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8734 (tp30)
REVERT: D  106 HIS cc_start: 0.7962 (m90) cc_final: 0.7576 (m90)
REVERT: F   25 ASN cc_start: 0.5995 (m110) cc_final: 0.5640 (m-40)
REVERT: F   59 LYS cc_start: 0.9560 (tptm) cc_final: 0.9335 (tptt)
REVERT: F   67 ARG cc_start: 0.8708 (ttm110) cc_final: 0.8251 (ttp-170)
REVERT: F   88 TYR cc_start: 0.8529 (m-10) cc_final: 0.7961 (m-10)
REVERT: G   84 GLN cc_start: 0.8690 (tp40) cc_final: 0.8333 (tt0)
REVERT: H   73 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8329 (tp30)
REVERT: H  106 HIS cc_start: 0.8365 (m90) cc_final: 0.7943 (m-70)
  outliers start: 29
  outliers final: 25
  residues processed: 138
  average time/residue: 0.2178
  time to fit residues: 45.0377
Evaluate side-chains
  142 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   93 GLN
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain E residue  123 ASP
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   26 ILE
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 55 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   chunk 76 optimal weight:   10.0000
   chunk 32 optimal weight:    5.9990
   chunk 53 optimal weight:    8.9990
   chunk 98 optimal weight:   10.0000
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 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 = 0.3575 r_free = 0.3575 target = 0.054384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.047379 restraints weight = 114852.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.048480 restraints weight = 71788.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.049223 restraints weight = 49500.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.6430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  12800  Z= 0.227
  Angle     :  0.751  17.550  18555  Z= 0.428
  Chirality :  0.042   0.345   2120
  Planarity :  0.005   0.039   1326
  Dihedral  : 32.154 168.277   4048
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 23.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 27.96 %
    Favored  : 67.57 %
  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: -0.15 (0.30), residues: 736
  helix:  0.55 (0.22), residues: 530
  sheet:  None (None), residues: 0
  loop : -1.67 (0.40), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.018   0.002   PHE F  61 
 TYR   0.014   0.002   TYR D  37 
 ARG   0.004   0.001   ARG G  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07056 (  771)
  hydrogen bonds       : angle       4.25450 ( 1911)
  covalent geometry    : bond        0.00490 (12800)
  covalent geometry    : angle       0.75059 (18555)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 1.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.5772 (m110) cc_final: 0.5444 (m110)
REVERT: B   67 ARG cc_start: 0.8709 (ttm110) cc_final: 0.8410 (mtm110)
REVERT: B   88 TYR cc_start: 0.8611 (m-10) cc_final: 0.7978 (m-10)
REVERT: C   61 GLU cc_start: 0.9031 (tp30) cc_final: 0.8603 (tm-30)
REVERT: D   56 MET cc_start: 0.7489 (tpt) cc_final: 0.7207 (tpt)
REVERT: D   73 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8603 (tp30)
REVERT: D  106 HIS cc_start: 0.8075 (m90) cc_final: 0.7853 (m90)
REVERT: F   25 ASN cc_start: 0.5996 (m110) cc_final: 0.5637 (m-40)
REVERT: F   88 TYR cc_start: 0.8501 (m-10) cc_final: 0.7962 (m-10)
REVERT: G   84 GLN cc_start: 0.8723 (tp40) cc_final: 0.8414 (tt0)
REVERT: H   73 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8436 (tp30)
  outliers start: 28
  outliers final: 26
  residues processed: 144
  average time/residue: 0.2721
  time to fit residues: 58.2239
Evaluate side-chains
  139 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 113
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   93 GLN
Chi-restraints excluded: chain E residue  123 ASP
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   26 ILE
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 84 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 93 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 85 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 86 optimal weight:   10.0000
   chunk 80 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   overall best weight:    6.3992

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 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 = 0.3531 r_free = 0.3531 target = 0.052233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.045420 restraints weight = 114824.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.046475 restraints weight = 71515.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.047212 restraints weight = 49313.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.6773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078  12800  Z= 0.299
  Angle     :  0.807  15.494  18555  Z= 0.462
  Chirality :  0.046   0.558   2120
  Planarity :  0.006   0.046   1326
  Dihedral  : 32.336 166.994   4048
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 31.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 28.75 %
    Favored  : 67.57 %
  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: -0.49 (0.29), residues: 736
  helix:  0.26 (0.22), residues: 526
  sheet:  None (None), residues: 0
  loop : -1.64 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS F  75 
 PHE   0.016   0.002   PHE A  78 
 TYR   0.019   0.002   TYR D  37 
 ARG   0.005   0.001   ARG G  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09189 (  771)
  hydrogen bonds       : angle       4.58404 ( 1911)
  covalent geometry    : bond        0.00645 (12800)
  covalent geometry    : angle       0.80675 (18555)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 1.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.5913 (m110) cc_final: 0.5581 (m110)
REVERT: B   67 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8281 (ttp-170)
REVERT: B   88 TYR cc_start: 0.8619 (m-10) cc_final: 0.7993 (m-10)
REVERT: C   61 GLU cc_start: 0.9074 (tp30) cc_final: 0.8830 (tm-30)
REVERT: D   56 MET cc_start: 0.7574 (tpt) cc_final: 0.7312 (tpt)
REVERT: D   73 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8723 (tp30)
REVERT: D  106 HIS cc_start: 0.8060 (m90) cc_final: 0.7742 (m90)
REVERT: F   88 TYR cc_start: 0.8416 (m-10) cc_final: 0.7937 (m-10)
REVERT: H   73 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8261 (tp30)
  outliers start: 23
  outliers final: 22
  residues processed: 133
  average time/residue: 0.2112
  time to fit residues: 42.3557
Evaluate side-chains
  134 residues out of total 626 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  123 ASP
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   21 VAL
Chi-restraints excluded: chain B residue   22 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   42 LEU
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  123 ASP
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   34 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   43 VAL
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   41 VAL
Chi-restraints excluded: chain H residue  103 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 56 optimal weight:    0.9990
   chunk 17 optimal weight:   20.0000
   chunk 76 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS
B  27 GLN
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** 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 = 0.3594 r_free = 0.3594 target = 0.055150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.048098 restraints weight = 112995.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.049224 restraints weight = 70366.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.049989 restraints weight = 48621.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.6733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  12800  Z= 0.205
  Angle     :  0.755  16.347  18555  Z= 0.427
  Chirality :  0.042   0.421   2120
  Planarity :  0.005   0.040   1326
  Dihedral  : 32.153 168.592   4048
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 21.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 30.35 %
    Favored  : 66.77 %
  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: -0.27 (0.30), residues: 736
  helix:  0.46 (0.22), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.71 (0.40), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.018   0.002   PHE F  61 
 TYR   0.018   0.002   TYR D  37 
 ARG   0.004   0.000   ARG G  32 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06384 (  771)
  hydrogen bonds       : angle       4.29801 ( 1911)
  covalent geometry    : bond        0.00445 (12800)
  covalent geometry    : angle       0.75465 (18555)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3283.77 seconds
wall clock time: 61 minutes 34.58 seconds (3694.58 seconds total)