Starting phenix.real_space_refine
on Wed Feb  4 16:41:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zjt_60156/02_2026/8zjt_60156.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zjt_60156/02_2026/8zjt_60156.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zjt_60156/02_2026/8zjt_60156.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zjt_60156/02_2026/8zjt_60156.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zjt_60156/02_2026/8zjt_60156.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zjt_60156/02_2026/8zjt_60156.map"
  }
  resolution = 3.2
  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=   0.002 sd=   0.071
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     278      5.49       5
     S      10      5.16       5
     C    6534      2.51       5
     N    2228      2.21       5
     O    2735      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11785
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 820
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 98, 809
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
      Conformer: "B"
        Number of residues, atoms: 98, 809
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          bond proxies already assigned to first conformer: 809
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 831
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 755
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 724
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 724
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 699
    Chain: "E"
      Number of atoms: 805
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 94, 772
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 3, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 94, 772
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 3, 'TRANS': 90}
          bond proxies already assigned to first conformer: 746
    Chain: "F"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 837
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 107, 826
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 107, 826
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 823
    Chain: "H"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 735
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2865
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2865
          Classifications: {'DNA': 139}
          Link IDs: {'rna3p': 138}
    Chain: "J"
      Number of atoms: 2834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2834
          Classifications: {'DNA': 139}
          Link IDs: {'rna3p': 138}
  Residues with excluded nonbonded symmetry interactions: 8
    residue:
      pdb=" N  AARG A  54 " occ=0.43
      ... (20 atoms not shown)
      pdb=" NH2BARG A  54 " occ=0.57
    residue:
      pdb=" N  AHIS D  83 " occ=0.56
      ... (18 atoms not shown)
      pdb=" NE2BHIS D  83 " occ=0.44
    residue:
      pdb=" N  AARG D  87 " occ=0.56
      ... (20 atoms not shown)
      pdb=" NH2BARG D  87 " occ=0.44
    residue:
      pdb=" N  AHIS D 110 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS D 110 " occ=0.50
    residue:
      pdb=" N  AARG E  43 " occ=0.35
      ... (20 atoms not shown)
      pdb=" NH2BARG E  43 " occ=0.65
    residue:
      pdb=" N  AARG E  53 " occ=0.47
      ... (20 atoms not shown)
      pdb=" NH2BARG E  53 " occ=0.53
    residue:
      pdb=" N  AARG E  64 " occ=0.59
      ... (20 atoms not shown)
      pdb=" NH2BARG E  64 " occ=0.41
    residue:
      pdb=" N  AARG G 100 " occ=0.52
      ... (20 atoms not shown)
      pdb=" NH2BARG G 100 " occ=0.48
  Time building chain proxies: 3.05, per 1000 atoms: 0.26
  Number of scatterers: 11785
  At special positions: 0
  Unit cell: (77.015, 117.105, 135.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     278     15.00
     O    2735      8.00
     N    2228      7.00
     C    6534      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: 0.96
  Conformation dependent library (CDL) restraints added in 488.4 milliseconds
  

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1428

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 9 sheets defined
      70.9% alpha, 2.6% beta
      138 base pairs and 234 stacking pairs defined.
    Time for finding SS restraints: 2.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 58
    Processing helix  chain 'A' and resid 64 through 76
    Processing helix  chain 'A' and resid 86 through 115
    Processing helix  chain 'A' and resid 121 through 133
    Processing helix  chain 'B' and resid 26 through 30
    Processing helix  chain 'B' and resid 31 through 43
    Processing helix  chain 'B' and resid 50 through 77
      removed outlier: 4.119A  pdb=" N   GLU B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA B  77 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 95
      removed outlier: 3.607A  pdb=" N   VAL B  87 " --> pdb=" O   THR B  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 17 through 22
    Processing helix  chain 'C' and resid 27 through 38
    Processing helix  chain 'C' and resid 46 through 74
      removed outlier: 4.345A  pdb=" N   VAL C  50 " --> pdb=" O   ALA C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 80 through 91
      removed outlier: 3.576A  pdb=" N   ASP C  91 " --> pdb=" O   ALA C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'D' and resid 38 through 50
    Processing helix  chain 'D' and resid 56 through 85
    Processing helix  chain 'D' and resid 91 through 103
      removed outlier: 3.538A  pdb=" N   ILE D  95 " --> pdb=" O   THR D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 123
    Processing helix  chain 'E' and resid 45 through 58
      removed outlier: 3.525A  pdb=" N   ARG E  50 " --> pdb=" O   THR E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 76
      removed outlier: 3.534A  pdb=" N   PHE E  68 " --> pdb=" O  AARG E  64 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 115
    Processing helix  chain 'E' and resid 121 through 133
    Processing helix  chain 'F' and resid 26 through 30
    Processing helix  chain 'F' and resid 31 through 42
    Processing helix  chain 'F' and resid 50 through 77
      removed outlier: 3.715A  pdb=" N   GLU F  54 " --> pdb=" O   LEU F  50 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLY F  57 " --> pdb=" O   GLU F  53 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ARG F  68 " --> pdb=" O   GLU F  64 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ALA F  77 " --> pdb=" O   TYR F  73 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 94
      removed outlier: 3.512A  pdb=" N   GLN F  94 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 22
    Processing helix  chain 'G' and resid 28 through 37
    Processing helix  chain 'G' and resid 47 through 74
    Processing helix  chain 'G' and resid 80 through 91
      removed outlier: 3.575A  pdb=" N   ASP G  91 " --> pdb=" O   ALA G  87 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 98
    Processing helix  chain 'H' and resid 40 through 50
    Processing helix  chain 'H' and resid 56 through 85
    Processing helix  chain 'H' and resid 91 through 103
    Processing helix  chain 'H' and resid 105 through 125
      removed outlier: 3.601A  pdb=" N   ALA H 125 " --> pdb=" O   LYS H 121 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85
      removed outlier: 7.143A  pdb=" N   ARG A  84 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 99
      removed outlier: 6.365A  pdb=" N   THR B  97 " --> pdb=" O   THR G 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.424A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103
      removed outlier: 6.712A  pdb=" N   THR C 102 " --> pdb=" O   TYR F  99 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85
      removed outlier: 7.452A  pdb=" N   ARG E  84 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120
    Processing sheet with id=AA9, first strand: chain 'G' and resid 78 through 79

    399 hydrogen bonds defined for protein.
    1189 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      351 hydrogen bonds
      702 hydrogen bond angles
      0 basepair planarities
      138 basepair parallelities
      234 stacking parallelities
  Total time for adding SS restraints: 2.31

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2569
        1.34 -     1.45: 3860
        1.45 -     1.57: 5562
        1.57 -     1.69: 554
        1.69 -     1.81: 20
  Bond restraints: 12565
  Sorted by residual:
  bond pdb=" C3'  DA J 137 "
       pdb=" O3'  DA J 137 "
    ideal  model  delta    sigma   weight residual
    1.422  1.463 -0.041 3.00e-02 1.11e+03 1.87e+00
  bond pdb=" CA  ASN G 111 "
       pdb=" CB  ASN G 111 "
    ideal  model  delta    sigma   weight residual
    1.533  1.564 -0.031 2.29e-02 1.91e+03 1.80e+00
  bond pdb=" CB  ASN G 111 "
       pdb=" CG  ASN G 111 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.40e+00
  bond pdb=" C3'  DT I 114 "
       pdb=" O3'  DT I 114 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.39e+00
  bond pdb=" C3'  DT J  15 "
       pdb=" O3'  DT J  15 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.32e+00
  ... (remaining 12560 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 17825
        1.84 -     3.68: 328
        3.68 -     5.52: 10
        5.52 -     7.36: 1
        7.36 -     9.20: 1
  Bond angle restraints: 18165
  Sorted by residual:
  angle pdb=" N   VAL G  28 "
        pdb=" CA  VAL G  28 "
        pdb=" C   VAL G  28 "
      ideal   model   delta    sigma   weight residual
     111.90  108.49    3.41 8.10e-01 1.52e+00 1.77e+01
  angle pdb=" CB  MET D  63 "
        pdb=" CG  MET D  63 "
        pdb=" SD  MET D  63 "
      ideal   model   delta    sigma   weight residual
     112.70  121.90   -9.20 3.00e+00 1.11e-01 9.41e+00
  angle pdb=" CA  ASN G 111 "
        pdb=" CB  ASN G 111 "
        pdb=" CG  ASN G 111 "
      ideal   model   delta    sigma   weight residual
     112.60  115.17   -2.57 1.00e+00 1.00e+00 6.60e+00
  angle pdb=" C   ASN G 111 "
        pdb=" CA  ASN G 111 "
        pdb=" CB  ASN G 111 "
      ideal   model   delta    sigma   weight residual
     109.37  114.21   -4.84 1.91e+00 2.74e-01 6.41e+00
  angle pdb=" C3'  DC I  74 "
        pdb=" C2'  DC I  74 "
        pdb=" C1'  DC I  74 "
      ideal   model   delta    sigma   weight residual
     101.60   98.13    3.47 1.50e+00 4.44e-01 5.36e+00
  ... (remaining 18160 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.26: 5460
       35.26 -    70.52: 1374
       70.52 -   105.79: 24
      105.79 -   141.05: 4
      141.05 -   176.31: 2
  Dihedral angle restraints: 6864
    sinusoidal: 4642
      harmonic: 2222
  Sorted by residual:
  dihedral pdb=" C4'  DT J  15 "
           pdb=" C3'  DT J  15 "
           pdb=" O3'  DT J  15 "
           pdb=" P    DG J  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   36.31 -176.31     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA J 137 "
           pdb=" C3'  DA J 137 "
           pdb=" O3'  DA J 137 "
           pdb=" P    DA J 138 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   48.32  171.68     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DG J  29 "
           pdb=" C3'  DG J  29 "
           pdb=" O3'  DG J  29 "
           pdb=" P    DC J  30 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   86.06  133.94     1      3.50e+01 8.16e-04 1.33e+01
  ... (remaining 6861 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1283
       0.025 -    0.050: 544
       0.050 -    0.075: 160
       0.075 -    0.100: 38
       0.100 -    0.125: 36
  Chirality restraints: 2061
  Sorted by residual:
  chirality pdb=" CA  ILE F  30 "
            pdb=" N   ILE F  30 "
            pdb=" C   ILE F  30 "
            pdb=" CB  ILE F  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.89e-01
  chirality pdb=" CA  ILE G 112 "
            pdb=" N   ILE G 112 "
            pdb=" C   ILE G 112 "
            pdb=" CB  ILE G 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" C3'  DA J 137 "
            pdb=" C4'  DA J 137 "
            pdb=" O3'  DA J 137 "
            pdb=" C2'  DA J 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.54   -0.12 2.00e-01 2.50e+01 3.86e-01
  ... (remaining 2058 not shown)

  Planarity restraints: 1343
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  77 "    0.022 2.00e-02 2.50e+03   9.27e-03 2.58e+00
        pdb=" N9   DG I  77 "   -0.020 2.00e-02 2.50e+03
        pdb=" C8   DG I  77 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7   DG I  77 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5   DG I  77 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DG I  77 "    0.002 2.00e-02 2.50e+03
        pdb=" O6   DG I  77 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DG I  77 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  77 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2   DG I  77 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I  77 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I  77 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU F  63 "    0.007 2.00e-02 2.50e+03   1.50e-02 2.24e+00
        pdb=" C   LEU F  63 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   LEU F  63 "    0.010 2.00e-02 2.50e+03
        pdb=" N   GLU F  64 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C  80 "    0.024 5.00e-02 4.00e+02   3.67e-02 2.16e+00
        pdb=" N   PRO C  81 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO C  81 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C  81 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1340 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1754
        2.76 -     3.30: 10427
        3.30 -     3.83: 23586
        3.83 -     4.37: 27077
        4.37 -     4.90: 39784
  Nonbonded interactions: 102628
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D  69 "
            pdb=" OH  TYR F  99 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" OG1 THR B  74 "
            pdb=" OD2 ASP B  86 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" NH2 ARG H  87 "
            pdb=" OP2  DC J  55 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" NH1 ARG G  82 "
            pdb=" O   VAL G 108 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" NH2 ARG B  36 "
            pdb=" OP2  DA J  96 "
     model   vdw
     2.299 3.120
  ... (remaining 102623 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 41 through 42 or resid 44 through 52 or resid 55 through 6 \ 
3 or resid 65 through 134))
  selection = (chain 'E' and (resid 41 through 42 or resid 44 through 52 or resid 55 through 6 \ 
3 or resid 65 through 134))
}
ncs_group {
  reference = (chain 'B' and resid 23 through 102)
  selection = (chain 'F' and resid 23 through 102)
}
ncs_group {
  reference = (chain 'C' and (resid 12 through 24 or resid 26 through 99 or resid 101 through  \ 
118))
  selection = (chain 'G' and (resid 12 through 99 or resid 101 through 118))
}
ncs_group {
  reference = (chain 'D' and (resid 33 through 82 or resid 84 through 86 or resid 88 through 1 \ 
09 or resid 111 through 125))
  selection = (chain 'H' and (resid 33 through 82 or resid 84 through 86 or resid 88 through 1 \ 
09 or resid 111 through 125))
}

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=0.35 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             2.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.280
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
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   0.041  12565  Z= 0.159
  Angle     :  0.536   9.202  18165  Z= 0.324
  Chirality :  0.033   0.125   2061
  Planarity :  0.004   0.037   1343
  Dihedral  : 28.713 176.311   5436
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  : 20.00 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.40 (0.31), residues: 763
  helix:  1.72 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -1.20 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 130 
 TYR   0.010   0.001   TYR G  58 
 PHE   0.006   0.001   PHE B  62 
 HIS   0.004   0.001   HIS G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (12565)
  covalent geometry    : angle       0.53561 (18165)
  hydrogen bonds       : bond        0.11141 (  750)
  hydrogen bonds       : angle       4.33436 ( 1891)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.333 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 76
  average time/residue: 0.1784
  time to fit residues: 17.3690
Evaluate side-chains
  76 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   57 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.3980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.168663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.106343 restraints weight = 64348.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.00
r_work: 0.2771 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2906
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2906
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.0631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12565  Z= 0.171
  Angle     :  0.548   6.665  18165  Z= 0.329
  Chirality :  0.034   0.131   2061
  Planarity :  0.004   0.039   1343
  Dihedral  : 31.300 176.835   3917
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 19.21 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.80 (0.30), residues: 763
  helix:  1.95 (0.22), residues: 561
  sheet:  None (None), residues: 0
  loop : -1.00 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 130 
 TYR   0.011   0.001   TYR H  38 
 PHE   0.007   0.001   PHE A  68 
 HIS   0.004   0.001   HIS G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (12565)
  covalent geometry    : angle       0.54795 (18165)
  hydrogen bonds       : bond        0.03842 (  750)
  hydrogen bonds       : angle       2.78013 ( 1891)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.310 
Fit side-chains
REVERT: A   91 MET cc_start: 0.8383 (tpp) cc_final: 0.7939 (mmt)
REVERT: C   74 ASN cc_start: 0.7362 (m-40) cc_final: 0.6766 (t0)
REVERT: D   63 MET cc_start: 0.8524 (mmm) cc_final: 0.8320 (mmp)
  outliers start: 4
  outliers final: 3
  residues processed: 80
  average time/residue: 0.1725
  time to fit residues: 17.9581
Evaluate side-chains
  76 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 94 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.3186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.166151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.121792 restraints weight = 57701.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 3.89
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3325
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3324
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.1032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12565  Z= 0.221
  Angle     :  0.576   6.466  18165  Z= 0.342
  Chirality :  0.036   0.129   2061
  Planarity :  0.004   0.039   1343
  Dihedral  : 31.640 177.138   3913
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 19.53 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.58 (0.30), residues: 763
  helix:  1.79 (0.22), residues: 560
  sheet:  None (None), residues: 0
  loop : -1.08 (0.41), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  72 
 TYR   0.012   0.002   TYR H  38 
 PHE   0.009   0.002   PHE A  68 
 HIS   0.004   0.001   HIS G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 (12565)
  covalent geometry    : angle       0.57626 (18165)
  hydrogen bonds       : bond        0.04089 (  750)
  hydrogen bonds       : angle       2.80847 ( 1891)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.308 
Fit side-chains
REVERT: D   63 MET cc_start: 0.8186 (mmm) cc_final: 0.7899 (mmp)
  outliers start: 9
  outliers final: 4
  residues processed: 81
  average time/residue: 0.1797
  time to fit residues: 18.6241
Evaluate side-chains
  77 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain D residue   86 LYS
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 95 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 55 optimal weight:    0.1980
   chunk 20 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 88 optimal weight:    3.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.169054 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.107303 restraints weight = 62587.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 1.85
r_work: 0.2775 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2924
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2924 r_free = 0.2924    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2924
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12565  Z= 0.162
  Angle     :  0.537   6.435  18165  Z= 0.323
  Chirality :  0.033   0.126   2061
  Planarity :  0.004   0.040   1343
  Dihedral  : 31.362 176.157   3913
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 19.37 %
    Favored  : 79.69 %
  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:  1.94 (0.30), residues: 763
  helix:  2.04 (0.22), residues: 561
  sheet:  None (None), residues: 0
  loop : -0.91 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  72 
 TYR   0.012   0.001   TYR D  41 
 PHE   0.006   0.001   PHE E  68 
 HIS   0.004   0.001   HIS G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (12565)
  covalent geometry    : angle       0.53680 (18165)
  hydrogen bonds       : bond        0.03540 (  750)
  hydrogen bonds       : angle       2.61377 ( 1891)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   91 MET cc_start: 0.8279 (tpp) cc_final: 0.7835 (mmt)
REVERT: A  130 ARG cc_start: 0.8517 (tpt-90) cc_final: 0.7430 (tpt90)
REVERT: C   74 ASN cc_start: 0.7305 (m-40) cc_final: 0.6729 (t0)
REVERT: D   63 MET cc_start: 0.8444 (mmm) cc_final: 0.8205 (mmp)
  outliers start: 5
  outliers final: 2
  residues processed: 80
  average time/residue: 0.1568
  time to fit residues: 16.3747
Evaluate side-chains
  76 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 96 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.3986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.166079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.104629 restraints weight = 56439.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.2923 rms_B_bonded: 1.79
r_work: 0.2730 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.1269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  12565  Z= 0.230
  Angle     :  0.578   6.027  18165  Z= 0.343
  Chirality :  0.036   0.141   2061
  Planarity :  0.004   0.040   1343
  Dihedral  : 31.653 176.563   3913
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 18.43 %
    Favored  : 79.69 %
  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:  1.65 (0.30), residues: 763
  helix:  1.85 (0.22), residues: 559
  sheet:  None (None), residues: 0
  loop : -1.02 (0.41), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  72 
 TYR   0.012   0.002   TYR H  38 
 PHE   0.009   0.002   PHE A  68 
 HIS   0.005   0.001   HIS G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 (12565)
  covalent geometry    : angle       0.57830 (18165)
  hydrogen bonds       : bond        0.04083 (  750)
  hydrogen bonds       : angle       2.76671 ( 1891)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.296 
Fit side-chains
REVERT: C   74 ASN cc_start: 0.7519 (m-40) cc_final: 0.6834 (t0)
REVERT: C   77 THR cc_start: 0.8889 (p) cc_final: 0.8576 (t)
REVERT: D   63 MET cc_start: 0.8487 (mmm) cc_final: 0.8242 (mmp)
  outliers start: 11
  outliers final: 7
  residues processed: 79
  average time/residue: 0.1648
  time to fit residues: 16.8938
Evaluate side-chains
  78 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain D residue   86 LYS
Chi-restraints excluded: chain E residue   57 LYS
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9980
   chunk 92 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.168316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.106421 restraints weight = 60228.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 1.87
r_work: 0.2753 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2903
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2903 r_free = 0.2903    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12565  Z= 0.176
  Angle     :  0.545   5.933  18165  Z= 0.327
  Chirality :  0.034   0.154   2061
  Planarity :  0.004   0.040   1343
  Dihedral  : 31.452 175.817   3913
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 19.21 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.93 (0.30), residues: 763
  helix:  2.01 (0.22), residues: 562
  sheet:  None (None), residues: 0
  loop : -0.83 (0.42), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  72 
 TYR   0.010   0.001   TYR G  58 
 PHE   0.006   0.001   PHE A  68 
 HIS   0.004   0.001   HIS G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (12565)
  covalent geometry    : angle       0.54464 (18165)
  hydrogen bonds       : bond        0.03611 (  750)
  hydrogen bonds       : angle       2.61965 ( 1891)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.287 
Fit side-chains
REVERT: C   74 ASN cc_start: 0.7345 (m-40) cc_final: 0.6725 (t0)
REVERT: C   77 THR cc_start: 0.8873 (p) cc_final: 0.8548 (t)
REVERT: D   63 MET cc_start: 0.8488 (mmm) cc_final: 0.8241 (mmp)
REVERT: F   51 ILE cc_start: 0.8872 (OUTLIER) cc_final: 0.8466 (pt)
  outliers start: 10
  outliers final: 7
  residues processed: 81
  average time/residue: 0.1692
  time to fit residues: 17.7518
Evaluate side-chains
  81 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain D residue   86 LYS
Chi-restraints excluded: chain E residue   57 LYS
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 4 optimal weight:    0.3980
   chunk 8 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.168941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.124695 restraints weight = 53401.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 3.94
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3310
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3310
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12565  Z= 0.168
  Angle     :  0.543   5.905  18165  Z= 0.326
  Chirality :  0.034   0.157   2061
  Planarity :  0.004   0.040   1343
  Dihedral  : 31.424 176.056   3913
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 19.84 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.04 (0.30), residues: 763
  helix:  2.08 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop : -0.78 (0.42), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  72 
 TYR   0.010   0.001   TYR G  58 
 PHE   0.007   0.001   PHE A  68 
 HIS   0.004   0.001   HIS G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (12565)
  covalent geometry    : angle       0.54287 (18165)
  hydrogen bonds       : bond        0.03554 (  750)
  hydrogen bonds       : angle       2.59400 ( 1891)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   91 MET cc_start: 0.7490 (tpp) cc_final: 0.7073 (mmt)
REVERT: A  130 ARG cc_start: 0.7947 (tpt-90) cc_final: 0.7153 (tpt90)
REVERT: C   74 ASN cc_start: 0.7449 (m-40) cc_final: 0.6840 (t0)
REVERT: C   77 THR cc_start: 0.8860 (p) cc_final: 0.8533 (t)
REVERT: D   63 MET cc_start: 0.8087 (mmm) cc_final: 0.7763 (mmp)
REVERT: F   51 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8245 (pt)
  outliers start: 6
  outliers final: 3
  residues processed: 80
  average time/residue: 0.1647
  time to fit residues: 17.1100
Evaluate side-chains
  78 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 93 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 73 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 89 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    1.5184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.165592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.104199 restraints weight = 57486.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 1.85
r_work: 0.2734 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2831 r_free = 0.2831    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2831
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053  12565  Z= 0.246
  Angle     :  0.594   6.465  18165  Z= 0.350
  Chirality :  0.037   0.159   2061
  Planarity :  0.004   0.039   1343
  Dihedral  : 31.694 176.298   3913
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 19.21 %
    Favored  : 78.74 %
  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:  1.72 (0.30), residues: 763
  helix:  1.88 (0.22), residues: 559
  sheet:  None (None), residues: 0
  loop : -0.93 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  72 
 TYR   0.013   0.002   TYR H  38 
 PHE   0.009   0.002   PHE A  68 
 HIS   0.004   0.001   HIS G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00581 (12565)
  covalent geometry    : angle       0.59397 (18165)
  hydrogen bonds       : bond        0.04167 (  750)
  hydrogen bonds       : angle       2.77929 ( 1891)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.299 
Fit side-chains
REVERT: F   51 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8598 (pt)
  outliers start: 12
  outliers final: 9
  residues processed: 77
  average time/residue: 0.1688
  time to fit residues: 16.8387
Evaluate side-chains
  81 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain B residue   75 GLU
Chi-restraints excluded: chain B residue   83 THR
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain D residue   86 LYS
Chi-restraints excluded: chain E residue   57 LYS
Chi-restraints excluded: chain E residue   91 MET
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 72 optimal weight:    7.9990
   chunk 33 optimal weight:    0.6980
   chunk 83 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    0.1980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.169809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.108811 restraints weight = 56410.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 1.71
r_work: 0.2820 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2970
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2970 r_free = 0.2970    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2970
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12565  Z= 0.159
  Angle     :  0.535   5.935  18165  Z= 0.322
  Chirality :  0.033   0.155   2061
  Planarity :  0.004   0.041   1343
  Dihedral  : 31.324 175.557   3913
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 20.00 %
    Favored  : 78.74 %
  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:  2.14 (0.30), residues: 763
  helix:  2.16 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop : -0.75 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  72 
 TYR   0.010   0.001   TYR G  58 
 PHE   0.005   0.001   PHE E  68 
 HIS   0.004   0.001   HIS G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (12565)
  covalent geometry    : angle       0.53501 (18165)
  hydrogen bonds       : bond        0.03443 (  750)
  hydrogen bonds       : angle       2.54049 ( 1891)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A   91 MET cc_start: 0.8262 (tpp) cc_final: 0.7819 (mmt)
REVERT: A  130 ARG cc_start: 0.8490 (tpt-90) cc_final: 0.7432 (tpt90)
REVERT: C   74 ASN cc_start: 0.7437 (m-40) cc_final: 0.6807 (t0)
REVERT: C   77 THR cc_start: 0.8872 (p) cc_final: 0.8602 (t)
REVERT: F   51 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8481 (pt)
REVERT: H   60 MET cc_start: 0.8439 (tpp) cc_final: 0.8174 (mmm)
  outliers start: 7
  outliers final: 3
  residues processed: 81
  average time/residue: 0.1468
  time to fit residues: 15.5584
Evaluate side-chains
  77 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 73
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.168785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.124691 restraints weight = 50289.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 3.87
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3313
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3313 r_free = 0.3313    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3313
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12565  Z= 0.178
  Angle     :  0.549   5.933  18165  Z= 0.328
  Chirality :  0.034   0.154   2061
  Planarity :  0.004   0.041   1343
  Dihedral  : 31.381 176.236   3913
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 20.00 %
    Favored  : 78.43 %
  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:  2.14 (0.30), residues: 763
  helix:  2.15 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop : -0.73 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  72 
 TYR   0.019   0.001   TYR D  41 
 PHE   0.007   0.001   PHE A  68 
 HIS   0.004   0.001   HIS G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (12565)
  covalent geometry    : angle       0.54901 (18165)
  hydrogen bonds       : bond        0.03613 (  750)
  hydrogen bonds       : angle       2.58329 ( 1891)

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

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

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1526 Ramachandran restraints generated.
    763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  130 ARG cc_start: 0.7941 (tpt-90) cc_final: 0.7202 (tpt90)
REVERT: C   74 ASN cc_start: 0.7337 (m-40) cc_final: 0.6796 (t0)
REVERT: C   77 THR cc_start: 0.8841 (p) cc_final: 0.8565 (t)
REVERT: E  130 ARG cc_start: 0.8094 (tpt90) cc_final: 0.7759 (tpt90)
REVERT: F   51 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8281 (pt)
REVERT: H   60 MET cc_start: 0.8138 (tpp) cc_final: 0.7832 (mmm)
  outliers start: 9
  outliers final: 7
  residues processed: 80
  average time/residue: 0.1588
  time to fit residues: 16.6119
Evaluate side-chains
  82 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 VAL
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain E residue   57 LYS
Chi-restraints excluded: chain E residue   91 MET
Chi-restraints excluded: chain F residue   50 LEU
Chi-restraints excluded: chain F residue   51 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  124 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 80 optimal weight:    4.9990
   chunk 84 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   chunk 97 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.169692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.124996 restraints weight = 46456.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 3.86
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3341
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12565  Z= 0.166
  Angle     :  0.540   5.912  18165  Z= 0.324
  Chirality :  0.033   0.159   2061
  Planarity :  0.004   0.041   1343
  Dihedral  : 31.318 176.079   3913
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 20.47 %
    Favored  : 78.43 %
  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:  2.21 (0.30), residues: 763
  helix:  2.20 (0.21), residues: 562
  sheet:  None (None), residues: 0
  loop : -0.67 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  72 
 TYR   0.021   0.001   TYR D  41 
 PHE   0.006   0.001   PHE A  68 
 HIS   0.004   0.001   HIS G  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (12565)
  covalent geometry    : angle       0.54018 (18165)
  hydrogen bonds       : bond        0.03519 (  750)
  hydrogen bonds       : angle       2.54509 ( 1891)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2534.04 seconds
wall clock time: 44 minutes 10.27 seconds (2650.27 seconds total)