Starting phenix.real_space_refine
on Fri Jul  3 05:41:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c4d_45182/07_2026/9c4d_45182.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c4d_45182/07_2026/9c4d_45182.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c4d_45182/07_2026/9c4d_45182.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c4d_45182/07_2026/9c4d_45182.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c4d_45182/07_2026/9c4d_45182.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c4d_45182/07_2026/9c4d_45182.cif"
  }
  resolution = 4.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.012
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: 6
    Type Number    sf(0)   Gaussians
     Mn     16      7.51       5
     P     154      5.49       5
     S      24      5.16       5
     C    7426      2.51       5
     N    2149      2.21       5
     O    2724      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12493
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1563
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1563
          Classifications: {'DNA': 77}
          Link IDs: {'rna3p': 76}
    Chain: "B"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1594
          Classifications: {'DNA': 77}
          Link IDs: {'rna3p': 76}
    Chain: "C"
      Number of atoms: 1165
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1165
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 137}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 0
          Ad-hoc single atom residues: {' MN': 2}
          Chain breaks: 2
  Restraints were copied for chains:
    D, E, F, G, H, I, J
  Time building chain proxies: 2.07, per 1000 atoms: 0.17
  Number of scatterers: 12493
  At special positions: 0
  Unit cell: (94.8537, 91.5255, 269.584, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn     16     24.99
     S      24     16.00
     P     154     15.00
     O    2724      8.00
     N    2149      7.00
     C    7426      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: 1.02
  Conformation dependent library (CDL) restraints added in 418.2 milliseconds
  

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      64 helices and 8 sheets defined
      84.4% alpha, 2.9% beta
      74 base pairs and 133 stacking pairs defined.
    Time for finding SS restraints: 1.55
  Creating SS restraints...
    Processing helix  chain 'C' and resid 3 through 21
      removed outlier: 3.662A  pdb=" N   GLU C   7 " --> pdb=" O   THR C   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 33
    Processing helix  chain 'C' and resid 35 through 49
    Processing helix  chain 'C' and resid 63 through 88
      removed outlier: 3.567A  pdb=" N   ILE C  87 " --> pdb=" O   PHE C  83 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY C  88 " --> pdb=" O   LEU C  84 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 102
      removed outlier: 4.172A  pdb=" N   TYR C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   ASN C  96 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 106 through 122
    Processing helix  chain 'C' and resid 124 through 139
    Processing helix  chain 'C' and resid 140 through 142
      No H-bonds generated for 'chain 'C' and resid 140 through 142'
    Processing helix  chain 'D' and resid 4 through 21
    Processing helix  chain 'D' and resid 24 through 33
    Processing helix  chain 'D' and resid 35 through 49
    Processing helix  chain 'D' and resid 63 through 88
      removed outlier: 3.567A  pdb=" N   ILE D  87 " --> pdb=" O   PHE D  83 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLY D  88 " --> pdb=" O   LEU D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 4.172A  pdb=" N   TYR D  95 " --> pdb=" O   GLU D  91 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ASN D  96 " --> pdb=" O   GLU D  92 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 106 through 122
    Processing helix  chain 'D' and resid 124 through 139
    Processing helix  chain 'D' and resid 140 through 142
      No H-bonds generated for 'chain 'D' and resid 140 through 142'
    Processing helix  chain 'E' and resid 4 through 21
    Processing helix  chain 'E' and resid 24 through 33
    Processing helix  chain 'E' and resid 35 through 49
    Processing helix  chain 'E' and resid 63 through 88
      removed outlier: 3.567A  pdb=" N   ILE E  87 " --> pdb=" O   PHE E  83 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLY E  88 " --> pdb=" O   LEU E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 102
      removed outlier: 4.171A  pdb=" N   TYR E  95 " --> pdb=" O   GLU E  91 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   ASN E  96 " --> pdb=" O   GLU E  92 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 106 through 122
    Processing helix  chain 'E' and resid 124 through 139
    Processing helix  chain 'E' and resid 140 through 142
      No H-bonds generated for 'chain 'E' and resid 140 through 142'
    Processing helix  chain 'F' and resid 4 through 21
    Processing helix  chain 'F' and resid 24 through 33
    Processing helix  chain 'F' and resid 35 through 49
    Processing helix  chain 'F' and resid 63 through 88
      removed outlier: 3.567A  pdb=" N   ILE F  87 " --> pdb=" O   PHE F  83 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY F  88 " --> pdb=" O   LEU F  84 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 90 through 102
      removed outlier: 4.173A  pdb=" N   TYR F  95 " --> pdb=" O   GLU F  91 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   ASN F  96 " --> pdb=" O   GLU F  92 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 106 through 122
    Processing helix  chain 'F' and resid 124 through 139
    Processing helix  chain 'F' and resid 140 through 142
      No H-bonds generated for 'chain 'F' and resid 140 through 142'
    Processing helix  chain 'G' and resid 4 through 21
    Processing helix  chain 'G' and resid 24 through 33
    Processing helix  chain 'G' and resid 35 through 49
    Processing helix  chain 'G' and resid 63 through 88
      removed outlier: 3.567A  pdb=" N   ILE G  87 " --> pdb=" O   PHE G  83 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY G  88 " --> pdb=" O   LEU G  84 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 102
      removed outlier: 4.172A  pdb=" N   TYR G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ASN G  96 " --> pdb=" O   GLU G  92 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 106 through 122
    Processing helix  chain 'G' and resid 124 through 139
    Processing helix  chain 'G' and resid 140 through 142
      No H-bonds generated for 'chain 'G' and resid 140 through 142'
    Processing helix  chain 'H' and resid 4 through 21
    Processing helix  chain 'H' and resid 24 through 33
    Processing helix  chain 'H' and resid 35 through 49
    Processing helix  chain 'H' and resid 63 through 88
      removed outlier: 3.567A  pdb=" N   ILE H  87 " --> pdb=" O   PHE H  83 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY H  88 " --> pdb=" O   LEU H  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 4.172A  pdb=" N   TYR H  95 " --> pdb=" O   GLU H  91 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ASN H  96 " --> pdb=" O   GLU H  92 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 106 through 122
    Processing helix  chain 'H' and resid 124 through 139
    Processing helix  chain 'H' and resid 140 through 142
      No H-bonds generated for 'chain 'H' and resid 140 through 142'
    Processing helix  chain 'I' and resid 4 through 21
    Processing helix  chain 'I' and resid 24 through 33
    Processing helix  chain 'I' and resid 35 through 49
    Processing helix  chain 'I' and resid 63 through 88
      removed outlier: 3.568A  pdb=" N   ILE I  87 " --> pdb=" O   PHE I  83 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLY I  88 " --> pdb=" O   LEU I  84 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 90 through 102
      removed outlier: 4.172A  pdb=" N   TYR I  95 " --> pdb=" O   GLU I  91 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ASN I  96 " --> pdb=" O   GLU I  92 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 106 through 122
    Processing helix  chain 'I' and resid 124 through 139
    Processing helix  chain 'I' and resid 140 through 142
      No H-bonds generated for 'chain 'I' and resid 140 through 142'
    Processing helix  chain 'J' and resid 4 through 21
    Processing helix  chain 'J' and resid 24 through 33
    Processing helix  chain 'J' and resid 35 through 49
    Processing helix  chain 'J' and resid 63 through 88
      removed outlier: 3.566A  pdb=" N   ILE J  87 " --> pdb=" O   PHE J  83 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLY J  88 " --> pdb=" O   LEU J  84 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 90 through 102
      removed outlier: 4.172A  pdb=" N   TYR J  95 " --> pdb=" O   GLU J  91 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   ASN J  96 " --> pdb=" O   GLU J  92 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 106 through 122
    Processing helix  chain 'J' and resid 124 through 139
    Processing helix  chain 'J' and resid 140 through 142
      No H-bonds generated for 'chain 'J' and resid 140 through 142'
    Processing sheet with id=AA1, first strand: chain 'C' and resid 52 through 54
    Processing sheet with id=AA2, first strand: chain 'D' and resid 52 through 54
    Processing sheet with id=AA3, first strand: chain 'E' and resid 52 through 54
    Processing sheet with id=AA4, first strand: chain 'F' and resid 52 through 54
    Processing sheet with id=AA5, first strand: chain 'G' and resid 52 through 54
    Processing sheet with id=AA6, first strand: chain 'H' and resid 52 through 54
    Processing sheet with id=AA7, first strand: chain 'I' and resid 52 through 54
    Processing sheet with id=AA8, first strand: chain 'J' and resid 52 through 54

    680 hydrogen bonds defined for protein.
    2040 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      172 hydrogen bonds
      344 hydrogen bond angles
      0 basepair planarities
      74 basepair parallelities
      133 stacking parallelities
  Total time for adding SS restraints: 1.98

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2516
        1.33 -     1.45: 3529
        1.45 -     1.57: 6621
        1.57 -     1.69: 306
        1.69 -     1.80: 48
  Bond restraints: 13020
  Sorted by residual:
  bond pdb=" C3'  DT B -43 "
       pdb=" C2'  DT B -43 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.06e+01
  bond pdb=" C3'  DC B -63 "
       pdb=" C2'  DC B -63 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.03e+01
  bond pdb=" C3'  DC A  74 "
       pdb=" C2'  DC A  74 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.01e+01
  bond pdb=" C3'  DA B -25 "
       pdb=" C2'  DA B -25 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.00e+01
  bond pdb=" C3'  DG B -62 "
       pdb=" C2'  DG B -62 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 9.36e+00
  ... (remaining 13015 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 17164
        1.30 -     2.59: 894
        2.59 -     3.89: 111
        3.89 -     5.18: 10
        5.18 -     6.48: 8
  Bond angle restraints: 18187
  Sorted by residual:
  angle pdb=" N3   DT B -57 "
        pdb=" C4   DT B -57 "
        pdb=" O4   DT B -57 "
      ideal   model   delta    sigma   weight residual
     119.90  122.64   -2.74 6.00e-01 2.78e+00 2.08e+01
  angle pdb=" N3   DT A  26 "
        pdb=" C4   DT A  26 "
        pdb=" O4   DT A  26 "
      ideal   model   delta    sigma   weight residual
     119.90  122.62   -2.72 6.00e-01 2.78e+00 2.05e+01
  angle pdb=" N3   DT B -11 "
        pdb=" C4   DT B -11 "
        pdb=" O4   DT B -11 "
      ideal   model   delta    sigma   weight residual
     119.90  122.60   -2.70 6.00e-01 2.78e+00 2.03e+01
  angle pdb=" N3   DT A  40 "
        pdb=" C4   DT A  40 "
        pdb=" O4   DT A  40 "
      ideal   model   delta    sigma   weight residual
     119.90  122.60   -2.70 6.00e-01 2.78e+00 2.02e+01
  angle pdb=" N3   DT A  16 "
        pdb=" C4   DT A  16 "
        pdb=" O4   DT A  16 "
      ideal   model   delta    sigma   weight residual
     119.90  122.59   -2.69 6.00e-01 2.78e+00 2.01e+01
  ... (remaining 18182 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.90: 6882
       35.90 -    71.80: 669
       71.80 -   107.70: 0
      107.70 -   143.60: 1
      143.60 -   179.50: 10
  Dihedral angle restraints: 7562
    sinusoidal: 4250
      harmonic: 3312
  Sorted by residual:
  dihedral pdb=" CA  GLU H  55 "
           pdb=" C   GLU H  55 "
           pdb=" N   LYS H  56 "
           pdb=" CA  LYS H  56 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.40  -21.60     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  GLU I  55 "
           pdb=" C   GLU I  55 "
           pdb=" N   LYS I  56 "
           pdb=" CA  LYS I  56 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.41  -21.59     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  GLU F  55 "
           pdb=" C   GLU F  55 "
           pdb=" N   LYS F  56 "
           pdb=" CA  LYS F  56 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.41  -21.59     0      5.00e+00 4.00e-02 1.87e+01
  ... (remaining 7559 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1331
       0.034 -    0.067: 476
       0.067 -    0.101: 130
       0.101 -    0.134: 47
       0.134 -    0.168: 8
  Chirality restraints: 1992
  Sorted by residual:
  chirality pdb=" C3'  DA A  60 "
            pdb=" C4'  DA A  60 "
            pdb=" O3'  DA A  60 "
            pdb=" C2'  DA A  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.56   -0.17 2.00e-01 2.50e+01 7.06e-01
  chirality pdb=" C3'  DC B -66 "
            pdb=" C4'  DC B -66 "
            pdb=" O3'  DC B -66 "
            pdb=" C2'  DC B -66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.57   -0.16 2.00e-01 2.50e+01 6.65e-01
  chirality pdb=" C3'  DA B -24 "
            pdb=" C4'  DA B -24 "
            pdb=" O3'  DA B -24 "
            pdb=" C2'  DA B -24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.58   -0.15 2.00e-01 2.50e+01 5.96e-01
  ... (remaining 1989 not shown)

  Planarity restraints: 1778
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT A  24 "    0.023 2.00e-02 2.50e+03   1.13e-02 3.17e+00
        pdb=" N1   DT A  24 "   -0.024 2.00e-02 2.50e+03
        pdb=" C2   DT A  24 "   -0.004 2.00e-02 2.50e+03
        pdb=" O2   DT A  24 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DT A  24 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DT A  24 "    0.005 2.00e-02 2.50e+03
        pdb=" O4   DT A  24 "    0.007 2.00e-02 2.50e+03
        pdb=" C5   DT A  24 "    0.001 2.00e-02 2.50e+03
        pdb=" C7   DT A  24 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DT A  24 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C  55 "    0.006 2.00e-02 2.50e+03   1.13e-02 1.27e+00
        pdb=" C   GLU C  55 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   GLU C  55 "    0.007 2.00e-02 2.50e+03
        pdb=" N   LYS C  56 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU I  55 "    0.005 2.00e-02 2.50e+03   1.12e-02 1.25e+00
        pdb=" C   GLU I  55 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   GLU I  55 "    0.007 2.00e-02 2.50e+03
        pdb=" N   LYS I  56 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1775 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.65: 248
        2.65 -     3.21: 11050
        3.21 -     3.77: 22212
        3.77 -     4.34: 27150
        4.34 -     4.90: 41222
  Nonbonded interactions: 101882
  Sorted by model distance:
  nonbonded pdb=" OP1  DT B -20 "
            pdb=" OH  TYR D  54 "
     model   vdw
     2.085 3.040
  nonbonded pdb=" OP1  DT A  27 "
            pdb=" NZ  LYS E  56 "
     model   vdw
     2.114 3.120
  nonbonded pdb=" OE1 GLU H 102 "
            pdb="MN    MN H 201 "
     model   vdw
     2.123 3.060
  nonbonded pdb=" OE1 GLU E 102 "
            pdb="MN    MN E 201 "
     model   vdw
     2.124 3.060
  nonbonded pdb=" OE1 GLU J 102 "
            pdb="MN    MN J 201 "
     model   vdw
     2.124 3.060
  ... (remaining 101877 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 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             9.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.090
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.010
  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:1.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
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      :  0.004   0.034  13020  Z= 0.366
  Angle     :  0.606   6.477  18187  Z= 0.528
  Chirality :  0.040   0.168   1992
  Planarity :  0.002   0.014   1778
  Dihedral  : 22.140 179.502   5434
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  :  3.91 %
    Favored  : 93.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  4.02 (0.26), residues: 1104
  helix:  3.09 (0.18), residues: 880
  sheet:  None (None), residues: 0
  loop :  0.86 (0.45), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG I 126 
 TYR   0.005   0.001   TYR D  75 
 PHE   0.003   0.001   PHE I 120 
 TRP   0.004   0.001   TRP F 107 
 HIS   0.002   0.001   HIS J 139 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00393 /  0.37 (13020)
  covalent geometry    : angle       0.60563 /  0.53 (18187)
  hydrogen bonds       : bond        0.10482 / 12.28 (  852)
  hydrogen bonds       : angle       4.13775 /  5.14 ( 2384)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 157
  time to evaluate  : 0.447 
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: D   42 MET cc_start: 0.8849 (tpp) cc_final: 0.7900 (tpp)
REVERT: E  112 ARG cc_start: 0.8147 (mmp80) cc_final: 0.7902 (mmp80)
REVERT: F   14 TYR cc_start: 0.7095 (t80) cc_final: 0.6879 (t80)
REVERT: F   51 TYR cc_start: 0.8041 (m-80) cc_final: 0.7621 (m-80)
REVERT: F   80 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8410 (tp)
REVERT: F   83 PHE cc_start: 0.8905 (t80) cc_final: 0.8606 (t80)
REVERT: H   15 MET cc_start: 0.9108 (ttp) cc_final: 0.8853 (ttm)
REVERT: H   42 MET cc_start: 0.8371 (tpp) cc_final: 0.8047 (tpp)
REVERT: I   51 TYR cc_start: 0.7619 (m-80) cc_final: 0.7234 (m-10)
REVERT: I  107 TRP cc_start: 0.5520 (m100) cc_final: 0.5280 (m100)
REVERT: J  107 TRP cc_start: 0.6915 (m100) cc_final: 0.6474 (t-100)
  outliers start: 24
  outliers final: 8
  residues processed: 179
  average time/residue: 0.1147
  time to fit residues: 29.1063
Evaluate side-chains
  84 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 123 optimal weight:    6.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 HIS
E 139 HIS
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 GLN
** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 139 HIS
** J  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.090624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.070760 restraints weight = 82318.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.069919 restraints weight = 59223.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.070361 restraints weight = 46332.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.070418 restraints weight = 35608.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.070561 restraints weight = 34517.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13020  Z= 0.206
  Angle     :  0.642  11.016  18187  Z= 0.366
  Chirality :  0.042   0.250   1992
  Planarity :  0.004   0.068   1778
  Dihedral  : 27.920 178.359   2986
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.76 %
    Favored  : 98.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.92 (0.25), residues: 1104
  helix:  2.43 (0.17), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.23 (0.43), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG I  76 
 TYR   0.017   0.002   TYR E   9 
 PHE   0.009   0.002   PHE H 120 
 TRP   0.013   0.002   TRP G 107 
 HIS   0.007   0.001   HIS F  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.21 (13020)
  covalent geometry    : angle       0.64189 /  0.37 (18187)
  hydrogen bonds       : bond        0.05556 /  6.24 (  852)
  hydrogen bonds       : angle       3.99426 /  4.96 ( 2384)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 84
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   42 MET cc_start: 0.8699 (tpp) cc_final: 0.8181 (tpp)
REVERT: F   42 MET cc_start: 0.8151 (tpt) cc_final: 0.7615 (tpp)
REVERT: F   78 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8347 (pp20)
REVERT: G    6 MET cc_start: 0.8556 (mtp) cc_final: 0.7998 (tmm)
REVERT: G   82 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8232 (tm-30)
REVERT: G  117 VAL cc_start: 0.8739 (t) cc_final: 0.8407 (t)
REVERT: G  142 GLN cc_start: 0.6991 (mt0) cc_final: 0.6611 (mp10)
REVERT: H   15 MET cc_start: 0.9039 (ttp) cc_final: 0.8825 (ttm)
REVERT: H   42 MET cc_start: 0.8401 (tpp) cc_final: 0.8087 (tpp)
REVERT: I   51 TYR cc_start: 0.7788 (m-80) cc_final: 0.7486 (m-10)
REVERT: J  107 TRP cc_start: 0.7434 (m100) cc_final: 0.6491 (t-100)
  outliers start: 2
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1317
  time to fit residues: 16.0047
Evaluate side-chains
  64 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 10 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 2 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 104 optimal weight:    0.4980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  77 HIS
** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  77 HIS
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 118 GLN
** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.090319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.069413 restraints weight = 81185.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.068569 restraints weight = 53677.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.068983 restraints weight = 46575.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.068968 restraints weight = 36501.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.069423 restraints weight = 33883.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  13020  Z= 0.160
  Angle     :  0.569   7.150  18187  Z= 0.330
  Chirality :  0.040   0.267   1992
  Planarity :  0.003   0.047   1778
  Dihedral  : 28.002 179.865   2986
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.93 %
    Favored  : 96.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.81 (0.26), residues: 1104
  helix:  2.38 (0.17), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.40 (0.44), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 112 
 TYR   0.016   0.001   TYR J   9 
 PHE   0.009   0.002   PHE J 120 
 TRP   0.006   0.001   TRP E 107 
 HIS   0.007   0.001   HIS C  77 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.16 (13020)
  covalent geometry    : angle       0.56909 /  0.33 (18187)
  hydrogen bonds       : bond        0.04608 /  5.07 (  852)
  hydrogen bonds       : angle       3.86797 /  4.79 ( 2384)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.297 
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: C   15 MET cc_start: 0.8457 (ppp) cc_final: 0.8223 (ppp)
REVERT: C   42 MET cc_start: 0.8715 (mmp) cc_final: 0.8226 (tpp)
REVERT: C   82 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8170 (pp30)
REVERT: D   42 MET cc_start: 0.8665 (tpp) cc_final: 0.8175 (tpp)
REVERT: F   42 MET cc_start: 0.8183 (tpt) cc_final: 0.7691 (tpp)
REVERT: F   51 TYR cc_start: 0.8275 (m-80) cc_final: 0.7729 (m-80)
REVERT: F  112 ARG cc_start: 0.8943 (mmp80) cc_final: 0.8658 (mmp80)
REVERT: G    6 MET cc_start: 0.8780 (mtp) cc_final: 0.8007 (tmm)
REVERT: G  142 GLN cc_start: 0.7080 (mt0) cc_final: 0.6712 (mp10)
REVERT: H   15 MET cc_start: 0.9042 (ttp) cc_final: 0.8839 (ttm)
REVERT: H   42 MET cc_start: 0.8522 (tpp) cc_final: 0.7986 (tpp)
REVERT: H   43 VAL cc_start: 0.9417 (t) cc_final: 0.9182 (p)
REVERT: I   51 TYR cc_start: 0.7768 (m-80) cc_final: 0.7369 (m-10)
REVERT: J  107 TRP cc_start: 0.7410 (m100) cc_final: 0.6552 (t-100)
  outliers start: 3
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1062
  time to fit residues: 13.3618
Evaluate side-chains
  62 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 111 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 124 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 56 optimal weight:    0.5980
   chunk 92 optimal weight:    1.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 118 GLN
** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  12 GLN
** J  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 134 GLN
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.089023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.064290 restraints weight = 79188.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.063895 restraints weight = 54338.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.064040 restraints weight = 44867.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.064324 restraints weight = 35936.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.064271 restraints weight = 32783.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13020  Z= 0.186
  Angle     :  0.609  11.079  18187  Z= 0.347
  Chirality :  0.042   0.273   1992
  Planarity :  0.004   0.069   1778
  Dihedral  : 28.087 179.711   2986
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.73 %
    Favored  : 97.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.78 (0.26), residues: 1104
  helix:  2.39 (0.17), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.54 (0.44), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG I  76 
 TYR   0.029   0.002   TYR J   9 
 PHE   0.014   0.002   PHE H 120 
 TRP   0.008   0.001   TRP F 107 
 HIS   0.005   0.001   HIS F  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.19 (13020)
  covalent geometry    : angle       0.60877 /  0.35 (18187)
  hydrogen bonds       : bond        0.04944 /  5.56 (  852)
  hydrogen bonds       : angle       3.90478 /  4.83 ( 2384)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 MET cc_start: 0.8919 (mmp) cc_final: 0.8234 (tpp)
REVERT: D    6 MET cc_start: 0.8602 (mmp) cc_final: 0.8219 (mmt)
REVERT: D   42 MET cc_start: 0.8922 (tpp) cc_final: 0.8425 (tpp)
REVERT: E    6 MET cc_start: 0.8035 (tmm) cc_final: 0.7818 (tmm)
REVERT: F   42 MET cc_start: 0.8373 (tpt) cc_final: 0.7871 (tpp)
REVERT: F   51 TYR cc_start: 0.8292 (m-80) cc_final: 0.7704 (m-80)
REVERT: F  112 ARG cc_start: 0.9199 (mmp80) cc_final: 0.8867 (mmp80)
REVERT: G  142 GLN cc_start: 0.7593 (mt0) cc_final: 0.7201 (mp10)
REVERT: H   42 MET cc_start: 0.8743 (tpp) cc_final: 0.8340 (tpp)
REVERT: I   51 TYR cc_start: 0.8301 (m-80) cc_final: 0.7874 (m-10)
REVERT: J  107 TRP cc_start: 0.7370 (m100) cc_final: 0.6607 (t-100)
  outliers start: 1
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1013
  time to fit residues: 12.0473
Evaluate side-chains
  59 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 122 optimal weight:    0.0050
   chunk 112 optimal weight:   10.0000
   chunk 56 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 32 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.5194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 134 GLN
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 134 GLN
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 118 GLN
** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  12 GLN
** J  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.089746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.068336 restraints weight = 81311.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.067448 restraints weight = 54285.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.067657 restraints weight = 49478.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.067776 restraints weight = 40172.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.068454 restraints weight = 35409.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  13020  Z= 0.133
  Angle     :  0.562   7.706  18187  Z= 0.320
  Chirality :  0.040   0.272   1992
  Planarity :  0.003   0.033   1778
  Dihedral  : 28.117 177.977   2986
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.56 %
    Favored  : 98.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.02 (0.26), residues: 1104
  helix:  2.56 (0.18), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.44 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  85 
 TYR   0.021   0.001   TYR J   9 
 PHE   0.013   0.001   PHE F 120 
 TRP   0.006   0.001   TRP F 107 
 HIS   0.004   0.001   HIS F  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.13 (13020)
  covalent geometry    : angle       0.56213 /  0.32 (18187)
  hydrogen bonds       : bond        0.04126 /  4.54 (  852)
  hydrogen bonds       : angle       3.80915 /  4.74 ( 2384)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   42 MET cc_start: 0.8830 (mmp) cc_final: 0.8343 (tpp)
REVERT: D    6 MET cc_start: 0.8164 (mmp) cc_final: 0.7795 (mmt)
REVERT: D   42 MET cc_start: 0.8857 (tpp) cc_final: 0.8351 (tpp)
REVERT: E    6 MET cc_start: 0.8053 (tmm) cc_final: 0.7830 (tmm)
REVERT: F   42 MET cc_start: 0.8211 (tpt) cc_final: 0.7780 (tpp)
REVERT: F   51 TYR cc_start: 0.8140 (m-80) cc_final: 0.7738 (m-80)
REVERT: F  112 ARG cc_start: 0.9207 (mmp80) cc_final: 0.8914 (mmp80)
REVERT: F  134 GLN cc_start: 0.8272 (pt0) cc_final: 0.7637 (mt0)
REVERT: G  142 GLN cc_start: 0.7278 (mt0) cc_final: 0.6911 (mp10)
REVERT: H   42 MET cc_start: 0.8632 (tpp) cc_final: 0.8177 (tpp)
REVERT: I   51 TYR cc_start: 0.8026 (m-80) cc_final: 0.7594 (m-10)
REVERT: J  107 TRP cc_start: 0.7410 (m100) cc_final: 0.6583 (t-100)
  outliers start: 1
  outliers final: 0
  residues processed: 83
  average time/residue: 0.0984
  time to fit residues: 12.1957
Evaluate side-chains
  59 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 5 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 121 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    1.1584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 103 HIS
H 118 GLN
** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  12 GLN
** J  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 134 GLN
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.087658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.065962 restraints weight = 81211.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.066345 restraints weight = 54845.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.066061 restraints weight = 42040.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.066048 restraints weight = 36656.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.066340 restraints weight = 32723.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  13020  Z= 0.206
  Angle     :  0.620   7.837  18187  Z= 0.354
  Chirality :  0.043   0.279   1992
  Planarity :  0.003   0.034   1778
  Dihedral  : 28.133 178.421   2986
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  1.46 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.66 (0.26), residues: 1104
  helix:  2.33 (0.17), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.72 (0.44), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  76 
 TYR   0.018   0.002   TYR F  14 
 PHE   0.011   0.002   PHE H 120 
 TRP   0.009   0.002   TRP F 107 
 HIS   0.005   0.001   HIS F  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00410 /  0.21 (13020)
  covalent geometry    : angle       0.61984 /  0.35 (18187)
  hydrogen bonds       : bond        0.05225 /  5.89 (  852)
  hydrogen bonds       : angle       3.96841 /  4.94 ( 2384)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.388 
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: C   15 MET cc_start: 0.8587 (ppp) cc_final: 0.8357 (ppp)
REVERT: C   42 MET cc_start: 0.8720 (mmp) cc_final: 0.8302 (tpp)
REVERT: D   42 MET cc_start: 0.8395 (tpp) cc_final: 0.7837 (tpp)
REVERT: E    6 MET cc_start: 0.8166 (tmm) cc_final: 0.7925 (tmm)
REVERT: F   42 MET cc_start: 0.8368 (tpt) cc_final: 0.7885 (tpp)
REVERT: F   51 TYR cc_start: 0.8207 (m-80) cc_final: 0.7774 (m-80)
REVERT: F  134 GLN cc_start: 0.8341 (pt0) cc_final: 0.7702 (mt0)
REVERT: H   42 MET cc_start: 0.8668 (tpp) cc_final: 0.8167 (tpp)
REVERT: I   51 TYR cc_start: 0.7515 (m-80) cc_final: 0.7205 (m-10)
REVERT: J  107 TRP cc_start: 0.7486 (m100) cc_final: 0.6601 (t-100)
REVERT: J  134 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7674 (mm-40)
  outliers start: 3
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1093
  time to fit residues: 12.2165
Evaluate side-chains
  58 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 60 optimal weight:    0.2980
   chunk 82 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 103 optimal weight:    0.7980
   chunk 88 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 108 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 11 optimal weight:    7.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 134 GLN
E  12 GLN
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.088206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.065554 restraints weight = 80434.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.064850 restraints weight = 59154.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.065495 restraints weight = 44115.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.065456 restraints weight = 37332.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.065509 restraints weight = 34137.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13020  Z= 0.150
  Angle     :  0.574   8.337  18187  Z= 0.327
  Chirality :  0.041   0.284   1992
  Planarity :  0.003   0.027   1778
  Dihedral  : 28.134 178.135   2986
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.68 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.82 (0.26), residues: 1104
  helix:  2.44 (0.18), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.65 (0.44), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG I 112 
 TYR   0.017   0.001   TYR F  14 
 PHE   0.011   0.001   PHE F 120 
 TRP   0.008   0.001   TRP F 107 
 HIS   0.005   0.001   HIS F  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.15 (13020)
  covalent geometry    : angle       0.57395 /  0.33 (18187)
  hydrogen bonds       : bond        0.04263 /  4.73 (  852)
  hydrogen bonds       : angle       3.89163 /  4.83 ( 2384)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.453 
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: C   15 MET cc_start: 0.8581 (ppp) cc_final: 0.8321 (ppp)
REVERT: C   42 MET cc_start: 0.8682 (mmp) cc_final: 0.8394 (tpt)
REVERT: D    6 MET cc_start: 0.8194 (mmp) cc_final: 0.7713 (mmt)
REVERT: D   42 MET cc_start: 0.8924 (tpp) cc_final: 0.8515 (tpp)
REVERT: E    6 MET cc_start: 0.8111 (tmm) cc_final: 0.7829 (tmm)
REVERT: E   42 MET cc_start: 0.7980 (tpp) cc_final: 0.7356 (tpt)
REVERT: F   42 MET cc_start: 0.8295 (tpt) cc_final: 0.7846 (tpp)
REVERT: F   51 TYR cc_start: 0.8190 (m-80) cc_final: 0.7749 (m-80)
REVERT: F   71 LYS cc_start: 0.9024 (tttt) cc_final: 0.8682 (pttm)
REVERT: F  134 GLN cc_start: 0.8344 (pt0) cc_final: 0.7688 (mt0)
REVERT: H   42 MET cc_start: 0.8679 (tpp) cc_final: 0.8098 (tpp)
REVERT: I   51 TYR cc_start: 0.7621 (m-80) cc_final: 0.7292 (m-10)
REVERT: J  106 SER cc_start: 0.6411 (t) cc_final: 0.6009 (t)
REVERT: J  107 TRP cc_start: 0.7464 (m100) cc_final: 0.6599 (t-100)
  outliers start: 1
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1036
  time to fit residues: 11.9806
Evaluate side-chains
  61 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 104 optimal weight:    5.9990
   chunk 91 optimal weight:    0.5980
   chunk 3 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 89 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0980
   chunk 40 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   chunk 124 optimal weight:    0.1980
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 GLN
** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.088422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.066538 restraints weight = 80609.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.066255 restraints weight = 54637.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.066777 restraints weight = 42213.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.066743 restraints weight = 35515.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.066738 restraints weight = 33431.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  13020  Z= 0.132
  Angle     :  0.564   7.225  18187  Z= 0.323
  Chirality :  0.040   0.284   1992
  Planarity :  0.003   0.028   1778
  Dihedral  : 28.116 178.201   2986
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.88 %
    Favored  : 99.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.90 (0.26), residues: 1104
  helix:  2.50 (0.18), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.63 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I  76 
 TYR   0.018   0.001   TYR F  14 
 PHE   0.009   0.001   PHE F 120 
 TRP   0.007   0.001   TRP F 107 
 HIS   0.005   0.001   HIS F  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.13 (13020)
  covalent geometry    : angle       0.56379 /  0.32 (18187)
  hydrogen bonds       : bond        0.04071 /  4.52 (  852)
  hydrogen bonds       : angle       3.83543 /  4.78 ( 2384)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.417 
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: C   15 MET cc_start: 0.8578 (ppp) cc_final: 0.8331 (ppp)
REVERT: C   42 MET cc_start: 0.8725 (mmp) cc_final: 0.8389 (tpt)
REVERT: D    6 MET cc_start: 0.8170 (mmp) cc_final: 0.7725 (mmt)
REVERT: D   42 MET cc_start: 0.8963 (tpp) cc_final: 0.8459 (tpp)
REVERT: E    6 MET cc_start: 0.8043 (tmm) cc_final: 0.7736 (tmm)
REVERT: E   42 MET cc_start: 0.8106 (tpp) cc_final: 0.7479 (tpt)
REVERT: F   42 MET cc_start: 0.8327 (tpt) cc_final: 0.7875 (tpp)
REVERT: F   51 TYR cc_start: 0.8196 (m-80) cc_final: 0.7728 (m-80)
REVERT: F   71 LYS cc_start: 0.9024 (tttt) cc_final: 0.8695 (pttm)
REVERT: F  134 GLN cc_start: 0.8331 (pt0) cc_final: 0.7656 (mt0)
REVERT: H   42 MET cc_start: 0.8724 (tpp) cc_final: 0.8200 (tpp)
REVERT: I   51 TYR cc_start: 0.7686 (m-80) cc_final: 0.7337 (m-10)
REVERT: J  106 SER cc_start: 0.6371 (t) cc_final: 0.6013 (t)
REVERT: J  107 TRP cc_start: 0.7455 (m100) cc_final: 0.6599 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1000
  time to fit residues: 11.5146
Evaluate side-chains
  61 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 70 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 102 optimal weight:    5.9990
   chunk 35 optimal weight:    0.5980
   chunk 14 optimal weight:    0.1980
   chunk 98 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9980
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 134 GLN
** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.088384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.064982 restraints weight = 80875.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.064226 restraints weight = 53348.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.064276 restraints weight = 42515.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.064470 restraints weight = 41442.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.064455 restraints weight = 35734.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.3724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13020  Z= 0.134
  Angle     :  0.561   7.810  18187  Z= 0.319
  Chirality :  0.040   0.287   1992
  Planarity :  0.003   0.028   1778
  Dihedral  : 28.095 178.520   2986
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.91 (0.26), residues: 1104
  helix:  2.51 (0.18), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.66 (0.45), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  72 
 TYR   0.010   0.001   TYR E  14 
 PHE   0.005   0.001   PHE H 120 
 TRP   0.007   0.001   TRP F 107 
 HIS   0.004   0.001   HIS E 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.13 (13020)
  covalent geometry    : angle       0.56131 /  0.32 (18187)
  hydrogen bonds       : bond        0.04061 /  4.52 (  852)
  hydrogen bonds       : angle       3.83715 /  4.80 ( 2384)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.418 
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: C   15 MET cc_start: 0.8628 (ppp) cc_final: 0.8398 (ppp)
REVERT: C   42 MET cc_start: 0.8882 (mmp) cc_final: 0.8437 (tpp)
REVERT: D   42 MET cc_start: 0.9001 (tpp) cc_final: 0.8328 (tpp)
REVERT: E    6 MET cc_start: 0.8160 (tmm) cc_final: 0.7883 (tmm)
REVERT: E   42 MET cc_start: 0.8139 (tpp) cc_final: 0.7512 (tpt)
REVERT: F   42 MET cc_start: 0.8395 (tpt) cc_final: 0.7903 (tpp)
REVERT: F   51 TYR cc_start: 0.8280 (m-80) cc_final: 0.7755 (m-80)
REVERT: F   71 LYS cc_start: 0.9065 (tttt) cc_final: 0.8693 (pttm)
REVERT: F  134 GLN cc_start: 0.8296 (pt0) cc_final: 0.7696 (mt0)
REVERT: H   42 MET cc_start: 0.8732 (tpp) cc_final: 0.8154 (tpp)
REVERT: I   51 TYR cc_start: 0.8137 (m-80) cc_final: 0.7827 (m-10)
REVERT: J  106 SER cc_start: 0.6485 (t) cc_final: 0.6060 (t)
REVERT: J  107 TRP cc_start: 0.7429 (m100) cc_final: 0.6664 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1056
  time to fit residues: 12.2043
Evaluate side-chains
  59 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 109 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 119 optimal weight:    1.9990
   chunk 42 optimal weight:    0.1980
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.087991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.065690 restraints weight = 80446.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.065096 restraints weight = 51800.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.065319 restraints weight = 40276.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.065359 restraints weight = 34506.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.065348 restraints weight = 34850.750|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.3879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13020  Z= 0.147
  Angle     :  0.577   9.230  18187  Z= 0.326
  Chirality :  0.041   0.300   1992
  Planarity :  0.003   0.027   1778
  Dihedral  : 28.067 178.498   2986
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.91 (0.26), residues: 1104
  helix:  2.52 (0.18), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.70 (0.46), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG I  76 
 TYR   0.011   0.001   TYR E  14 
 PHE   0.025   0.001   PHE F 120 
 TRP   0.007   0.001   TRP F 107 
 HIS   0.005   0.001   HIS F  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.15 (13020)
  covalent geometry    : angle       0.57744 /  0.33 (18187)
  hydrogen bonds       : bond        0.04232 /  4.74 (  852)
  hydrogen bonds       : angle       3.87058 /  4.80 ( 2384)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.427 
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: C   15 MET cc_start: 0.8610 (ppp) cc_final: 0.8371 (ppp)
REVERT: C   42 MET cc_start: 0.8818 (mmp) cc_final: 0.8404 (tpp)
REVERT: D   42 MET cc_start: 0.9102 (tpp) cc_final: 0.8637 (tpp)
REVERT: E    6 MET cc_start: 0.8218 (tmm) cc_final: 0.7928 (tmm)
REVERT: E   42 MET cc_start: 0.8190 (tpp) cc_final: 0.7560 (tpt)
REVERT: F   42 MET cc_start: 0.8403 (tpt) cc_final: 0.7908 (tpp)
REVERT: F   71 LYS cc_start: 0.9053 (tttt) cc_final: 0.8686 (pttm)
REVERT: F  134 GLN cc_start: 0.8329 (pt0) cc_final: 0.7672 (mt0)
REVERT: H   42 MET cc_start: 0.8833 (tpp) cc_final: 0.8410 (tpp)
REVERT: I   51 TYR cc_start: 0.7912 (m-80) cc_final: 0.7697 (m-10)
REVERT: J  106 SER cc_start: 0.6413 (t) cc_final: 0.6037 (t)
REVERT: J  107 TRP cc_start: 0.7462 (m100) cc_final: 0.6622 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0979
  time to fit residues: 11.3163
Evaluate side-chains
  61 residues out of total 1024 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 3 optimal weight:    8.9990
   chunk 41 optimal weight:    0.6980
   chunk 74 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0270
   chunk 43 optimal weight:    0.5980
   chunk 78 optimal weight:    0.0670
   chunk 103 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 7 optimal weight:   30.0000
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.4576

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 GLN
** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.088332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.066701 restraints weight = 80505.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.066091 restraints weight = 56606.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.066608 restraints weight = 42988.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.066590 restraints weight = 34695.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.066873 restraints weight = 32976.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.3947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  13020  Z= 0.124
  Angle     :  0.549   7.697  18187  Z= 0.313
  Chirality :  0.040   0.301   1992
  Planarity :  0.003   0.028   1778
  Dihedral  : 28.050 178.140   2986
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.01 (0.26), residues: 1104
  helix:  2.59 (0.18), residues: 888
  sheet:  None (None), residues: 0
  loop : -0.67 (0.46), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  85 
 TYR   0.014   0.001   TYR C  51 
 PHE   0.013   0.001   PHE F 120 
 TRP   0.007   0.001   TRP F 107 
 HIS   0.004   0.001   HIS E 103 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00218 /  0.12 (13020)
  covalent geometry    : angle       0.54929 /  0.31 (18187)
  hydrogen bonds       : bond        0.03881 /  4.29 (  852)
  hydrogen bonds       : angle       3.78449 /  4.67 ( 2384)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2102.76 seconds
wall clock time: 37 minutes 10.90 seconds (2230.90 seconds total)