Starting phenix.real_space_refine
on Sat Jul  4 13:59:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xaq_33097/07_2026/7xaq_33097.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xaq_33097/07_2026/7xaq_33097.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xaq_33097/07_2026/7xaq_33097.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xaq_33097/07_2026/7xaq_33097.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xaq_33097/07_2026/7xaq_33097.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xaq_33097/07_2026/7xaq_33097.cif"
  }
  resolution = 3.59
  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=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 9808 atoms to isotropic.
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     172      5.49       5
     S      42      5.16       5
     C    8005      2.51       5
     N    2379      2.21       5
     O    2798      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 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: 13396
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "F"
      Number of atoms: 880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 880
          Classifications: {'DNA': 43}
          Link IDs: {'rna3p': 42}
    Chain: "J"
      Number of atoms: 883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 883
          Classifications: {'DNA': 43}
          Link IDs: {'rna3p': 42}
    Chain: "E"
      Number of atoms: 880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 880
          Classifications: {'DNA': 43}
          Link IDs: {'rna3p': 42}
    Chain: "I"
      Number of atoms: 883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 883
          Classifications: {'DNA': 43}
          Link IDs: {'rna3p': 42}
    Chain: "B"
      Number of atoms: 1658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1658
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 6, 'TRANS': 194}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "A"
      Number of atoms: 1626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1626
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 192}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "G"
      Number of atoms: 1667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1667
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 194}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 1626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1626
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 192}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "H"
      Number of atoms: 1667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1667
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 6, 'TRANS': 194}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "D"
      Number of atoms: 1626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1626
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 192}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 17
  Time building chain proxies: 3.24, per 1000 atoms: 0.24
  Number of scatterers: 13396
  At special positions: 0
  Unit cell: (249.05, 156.4, 96.05, 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      42     16.00
     P     172     15.00
     O    2798      8.00
     N    2379      7.00
     C    8005      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: 1.15
  Conformation dependent library (CDL) restraints added in 445.7 milliseconds
  

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2286

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 0 sheets defined
      79.5% alpha, 0.0% beta
      72 base pairs and 115 stacking pairs defined.
    Time for finding SS restraints: 1.73
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 27
      removed outlier: 3.579A  pdb=" N   LEU B  23 " --> pdb=" O   LEU B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 35 through 42
    Processing helix  chain 'B' and resid 48 through 53
    Processing helix  chain 'B' and resid 57 through 77
      removed outlier: 4.627A  pdb=" N   ARG B  63 " --> pdb=" O   GLU B  59 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   HIS B  77 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 97
    Processing helix  chain 'B' and resid 100 through 113
    Processing helix  chain 'B' and resid 119 through 148
      removed outlier: 4.899A  pdb=" N   GLU B 125 " --> pdb=" O   GLU B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 173
      removed outlier: 4.180A  pdb=" N   HIS B 158 " --> pdb=" O   PRO B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 184
      removed outlier: 3.749A  pdb=" N   ASP B 184 " --> pdb=" O   GLU B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 198
      removed outlier: 4.014A  pdb=" N   HIS B 190 " --> pdb=" O   GLU B 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 8 through 29
    Processing helix  chain 'A' and resid 39 through 44
    Processing helix  chain 'A' and resid 48 through 54
    Processing helix  chain 'A' and resid 59 through 76
      removed outlier: 5.675A  pdb=" N   MET A  65 " --> pdb=" O   TYR A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 98
    Processing helix  chain 'A' and resid 99 through 114
      removed outlier: 4.041A  pdb=" N   TYR A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 147
    Processing helix  chain 'A' and resid 155 through 175
      removed outlier: 3.658A  pdb=" N   ALA A 169 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA A 171 " --> pdb=" O   HIS A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 198
    Processing helix  chain 'G' and resid 5 through 29
      removed outlier: 4.121A  pdb=" N   LYS G  24 " --> pdb=" O   ASP G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 35 through 44
      removed outlier: 3.795A  pdb=" N   GLY G  44 " --> pdb=" O   ALA G  40 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 52
      removed outlier: 3.814A  pdb=" N   ILE G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 56 through 77
      removed outlier: 3.520A  pdb=" N   ILE G  60 " --> pdb=" O   SER G  56 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 83
    Processing helix  chain 'G' and resid 84 through 98
      removed outlier: 3.810A  pdb=" N   LEU G  88 " --> pdb=" O   ASP G  84 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 99 through 114
      removed outlier: 3.593A  pdb=" N   GLU G 111 " --> pdb=" O   ASP G 107 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 119 through 148
    Processing helix  chain 'G' and resid 154 through 173
      removed outlier: 4.309A  pdb=" N   HIS G 158 " --> pdb=" O   PRO G 154 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 178 through 183
    Processing helix  chain 'G' and resid 185 through 198
    Processing helix  chain 'C' and resid 8 through 29
    Processing helix  chain 'C' and resid 35 through 44
      removed outlier: 3.931A  pdb=" N   ILE C  39 " --> pdb=" O   THR C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 52
    Processing helix  chain 'C' and resid 56 through 76
    Processing helix  chain 'C' and resid 85 through 98
    Processing helix  chain 'C' and resid 99 through 114
      removed outlier: 3.864A  pdb=" N   GLU C 111 " --> pdb=" O   ASP C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 148
      removed outlier: 3.725A  pdb=" N   VAL C 123 " --> pdb=" O   VAL C 119 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ASP C 147 " --> pdb=" O   GLU C 143 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLY C 148 " --> pdb=" O   ARG C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 154 through 173
      removed outlier: 3.987A  pdb=" N   HIS C 158 " --> pdb=" O   PRO C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 177 through 183
      removed outlier: 3.741A  pdb=" N   VAL C 181 " --> pdb=" O   PHE C 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 198
    Processing helix  chain 'H' and resid 5 through 29
    Processing helix  chain 'H' and resid 35 through 44
      removed outlier: 3.568A  pdb=" N   ILE H  39 " --> pdb=" O   THR H  35 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 46 through 51
    Processing helix  chain 'H' and resid 56 through 76
      removed outlier: 3.833A  pdb=" N   ILE H  60 " --> pdb=" O   SER H  56 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 80 through 83
    Processing helix  chain 'H' and resid 84 through 97
      removed outlier: 4.270A  pdb=" N   LEU H  88 " --> pdb=" O   ASP H  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 99 through 116
      removed outlier: 3.646A  pdb=" N   THR H 116 " --> pdb=" O   LYS H 112 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 120 through 146
    Processing helix  chain 'H' and resid 154 through 175
      removed outlier: 3.995A  pdb=" N   HIS H 158 " --> pdb=" O   PRO H 154 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 178 through 183
    Processing helix  chain 'H' and resid 185 through 198
      removed outlier: 3.624A  pdb=" N   PHE H 189 " --> pdb=" O   GLN H 185 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 30
    Processing helix  chain 'D' and resid 35 through 44
    Processing helix  chain 'D' and resid 47 through 52
    Processing helix  chain 'D' and resid 57 through 76
      removed outlier: 3.822A  pdb=" N   TYR D  61 " --> pdb=" O   LYS D  57 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 84 through 98
    Processing helix  chain 'D' and resid 99 through 114
    Processing helix  chain 'D' and resid 119 through 147
      removed outlier: 3.636A  pdb=" N   VAL D 123 " --> pdb=" O   VAL D 119 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASP D 147 " --> pdb=" O   GLU D 143 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 154 through 173
      removed outlier: 4.100A  pdb=" N   HIS D 158 " --> pdb=" O   PRO D 154 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 178 through 183
    Processing helix  chain 'D' and resid 185 through 198

    676 hydrogen bonds defined for protein.
    2013 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      182 hydrogen bonds
      364 hydrogen bond angles
      0 basepair planarities
      72 basepair parallelities
      115 stacking parallelities
  Total time for adding SS restraints: 2.26

  Time building geometry restraints manager: 1.59 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1929
        1.32 -     1.44: 4660
        1.44 -     1.57: 7033
        1.57 -     1.69: 341
        1.69 -     1.82: 78
  Bond restraints: 14041
  Sorted by residual:
  bond pdb=" N   ASP B  99 "
       pdb=" CA  ASP B  99 "
    ideal  model  delta    sigma   weight residual
    1.460  1.417  0.044 7.10e-03 1.98e+04 3.79e+01
  bond pdb=" CA  ASP B  99 "
       pdb=" C   ASP B  99 "
    ideal  model  delta    sigma   weight residual
    1.534  1.477  0.057 9.50e-03 1.11e+04 3.59e+01
  bond pdb=" C1'  DT F  36 "
       pdb=" N1   DT F  36 "
    ideal  model  delta    sigma   weight residual
    1.468  1.538 -0.070 1.40e-02 5.10e+03 2.47e+01
  bond pdb=" C1'  DT E  36 "
       pdb=" N1   DT E  36 "
    ideal  model  delta    sigma   weight residual
    1.468  1.537 -0.069 1.40e-02 5.10e+03 2.46e+01
  bond pdb=" C1'  DT F  33 "
       pdb=" N1   DT F  33 "
    ideal  model  delta    sigma   weight residual
    1.468  1.535 -0.067 1.40e-02 5.10e+03 2.30e+01
  ... (remaining 14036 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.15: 19277
        3.15 -     6.30: 346
        6.30 -     9.45: 29
        9.45 -    12.60: 5
       12.60 -    15.75: 2
  Bond angle restraints: 19659
  Sorted by residual:
  angle pdb=" N   THR A  49 "
        pdb=" CA  THR A  49 "
        pdb=" C   THR A  49 "
      ideal   model   delta    sigma   weight residual
     111.82  100.25   11.57 1.16e+00 7.43e-01 9.95e+01
  angle pdb=" N   ASP B  71 "
        pdb=" CA  ASP B  71 "
        pdb=" C   ASP B  71 "
      ideal   model   delta    sigma   weight residual
     112.38  102.44    9.94 1.22e+00 6.72e-01 6.63e+01
  angle pdb=" N   GLU A 183 "
        pdb=" CA  GLU A 183 "
        pdb=" C   GLU A 183 "
      ideal   model   delta    sigma   weight residual
     113.41  103.49    9.92 1.22e+00 6.72e-01 6.61e+01
  angle pdb=" N   GLN B 101 "
        pdb=" CA  GLN B 101 "
        pdb=" C   GLN B 101 "
      ideal   model   delta    sigma   weight residual
     110.80   95.05   15.75 2.13e+00 2.20e-01 5.47e+01
  angle pdb=" N   VAL A  34 "
        pdb=" CA  VAL A  34 "
        pdb=" C   VAL A  34 "
      ideal   model   delta    sigma   weight residual
     110.21  101.91    8.30 1.13e+00 7.83e-01 5.39e+01
  ... (remaining 19654 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.29: 6964
       31.29 -    62.57: 974
       62.57 -    93.86: 45
       93.86 -   125.14: 0
      125.14 -   156.43: 2
  Dihedral angle restraints: 7985
    sinusoidal: 4460
      harmonic: 3525
  Sorted by residual:
  dihedral pdb=" CA  TYR A  61 "
           pdb=" C   TYR A  61 "
           pdb=" N   LEU A  62 "
           pdb=" CA  LEU A  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.28   29.72     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" CA  TYR A  51 "
           pdb=" C   TYR A  51 "
           pdb=" N   LYS A  52 "
           pdb=" CA  LYS A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.32   29.68     0      5.00e+00 4.00e-02 3.52e+01
  dihedral pdb=" CA  GLY D  48 "
           pdb=" C   GLY D  48 "
           pdb=" N   THR D  49 "
           pdb=" CA  THR D  49 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.99   29.01     0      5.00e+00 4.00e-02 3.37e+01
  ... (remaining 7982 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1867
       0.091 -    0.182: 220
       0.182 -    0.272: 18
       0.272 -    0.363: 6
       0.363 -    0.454: 4
  Chirality restraints: 2115
  Sorted by residual:
  chirality pdb=" CA  PRO G   5 "
            pdb=" N   PRO G   5 "
            pdb=" C   PRO G   5 "
            pdb=" CB  PRO G   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.26    0.45 2.00e-01 2.50e+01 5.15e+00
  chirality pdb=" C3'  DT J   2 "
            pdb=" C4'  DT J   2 "
            pdb=" O3'  DT J   2 "
            pdb=" C2'  DT J   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.31   -0.42 2.00e-01 2.50e+01 4.50e+00
  chirality pdb=" CA  GLU A 183 "
            pdb=" N   GLU A 183 "
            pdb=" C   GLU A 183 "
            pdb=" CB  GLU A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.89   -0.38 2.00e-01 2.50e+01 3.55e+00
  ... (remaining 2112 not shown)

  Planarity restraints: 1934
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  98 "    0.021 2.00e-02 2.50e+03   4.41e-02 1.94e+01
        pdb=" C   ARG B  98 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   ARG B  98 "    0.030 2.00e-02 2.50e+03
        pdb=" N   ASP B  99 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS G  77 "   -0.019 2.00e-02 2.50e+03   4.02e-02 1.61e+01
        pdb=" C   HIS G  77 "    0.069 2.00e-02 2.50e+03
        pdb=" O   HIS G  77 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   SER G  78 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  32 "    0.042 2.00e-02 2.50e+03   2.48e-02 1.54e+01
        pdb=" N1   DT I  32 "   -0.063 2.00e-02 2.50e+03
        pdb=" C2   DT I  32 "   -0.009 2.00e-02 2.50e+03
        pdb=" O2   DT I  32 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DT I  32 "    0.017 2.00e-02 2.50e+03
        pdb=" C4   DT I  32 "    0.009 2.00e-02 2.50e+03
        pdb=" O4   DT I  32 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DT I  32 "   -0.000 2.00e-02 2.50e+03
        pdb=" C7   DT I  32 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DT I  32 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1931 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 58
        2.42 -     3.04: 8276
        3.04 -     3.66: 23566
        3.66 -     4.28: 34081
        4.28 -     4.90: 50703
  Nonbonded interactions: 116684
  Sorted by model distance:
  nonbonded pdb=" O   HIS G  77 "
            pdb=" OE2 GLU G  79 "
     model   vdw
     1.800 3.040
  nonbonded pdb=" C   PRO B 100 "
            pdb=" N   ARG B 102 "
     model   vdw
     1.932 3.350
  nonbonded pdb=" O   ILE D  45 "
            pdb=" OG1 THR D  49 "
     model   vdw
     1.980 3.040
  nonbonded pdb=" O   GLU B  17 "
            pdb=" OG1 THR B  21 "
     model   vdw
     2.004 3.040
  nonbonded pdb=" O   PHE D 134 "
            pdb=" OG1 THR D 138 "
     model   vdw
     2.045 3.040
  ... (remaining 116679 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 7 through 8 or (resid 9 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 10 through 204))
  selection = (chain 'B' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 8 through 77 or (resid 78 through 83 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 84 through 202 or (resid 203 through 204 and ( \ 
name N or name CA or name C or name O or name CB ))))
  selection = (chain 'C' and (resid 7 through 8 or (resid 9 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 10 through 204))
  selection = (chain 'D' and (resid 7 through 8 or (resid 9 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 10 through 204))
  selection = (chain 'G' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 8 through 77 or (resid 78 through 83 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 84 through 202 or (resid 203 through 204 and ( \ 
name N or name CA or name C or name O or name CB ))))
  selection = (chain 'H' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 8 through 77 or (resid 78 through 83 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 84 through 202 or (resid 203 through 204 and ( \ 
name N or name CA or name C or name O or name CB ))))
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = 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:             4.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.620
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5290
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      :  0.007   0.073  14041  Z= 0.556
  Angle     :  1.074  15.751  19659  Z= 0.760
  Chirality :  0.062   0.454   2115
  Planarity :  0.006   0.054   1934
  Dihedral  : 23.456 156.429   5699
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.81 %
    Favored  : 87.93 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  :  4.35 %
    Favored  : 92.78 %
  Cbeta Deviations :  0.09 %
  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: -4.12 (0.21), residues: 1185
  helix: -2.39 (0.14), residues: 866
  sheet:  None (None), residues: 0
  loop : -3.15 (0.35), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 102 
 TYR   0.025   0.003   TYR B 159 
 PHE   0.034   0.003   PHE A  26 
 TRP   0.010   0.002   TRP C 163 
 HIS   0.006   0.001   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00747 /  0.56 (14041)
  covalent geometry    : angle       1.07438 /  0.76 (19659)
  hydrogen bonds       : bond        0.12099 / 12.61 (  858)
  hydrogen bonds       : angle       6.50930 /  8.55 ( 2377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 0.465 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   20 ASP cc_start: 0.6144 (m-30) cc_final: 0.5900 (t0)
REVERT: B   66 LEU cc_start: 0.8897 (mt) cc_final: 0.8354 (mt)
REVERT: B   85 LYS cc_start: -0.1364 (OUTLIER) cc_final: -0.1692 (mmtt)
REVERT: B  101 GLN cc_start: 0.4956 (OUTLIER) cc_final: 0.4635 (tm-30)
REVERT: B  126 LEU cc_start: 0.5024 (mp) cc_final: 0.4569 (tt)
REVERT: B  191 PHE cc_start: 0.5872 (t80) cc_final: 0.5494 (t80)
REVERT: B  198 ARG cc_start: 0.6576 (mtm110) cc_final: 0.6069 (mmm-85)
REVERT: A   97 MET cc_start: 0.7757 (mtm) cc_final: 0.7287 (ttp)
REVERT: A  167 HIS cc_start: 0.5832 (t-90) cc_final: 0.5614 (t-90)
REVERT: A  177 PHE cc_start: 0.5628 (OUTLIER) cc_final: 0.4935 (t80)
REVERT: G   38 MET cc_start: 0.8025 (ttm) cc_final: 0.7621 (mtp)
REVERT: G  127 HIS cc_start: 0.9041 (m-70) cc_final: 0.8749 (m-70)
REVERT: G  128 LYS cc_start: 0.9262 (ptmt) cc_final: 0.9061 (ptpp)
REVERT: G  199 MET cc_start: 0.1008 (ppp) cc_final: 0.0010 (ppp)
REVERT: C  199 MET cc_start: 0.2544 (mtm) cc_final: 0.0258 (mmm)
REVERT: H   65 MET cc_start: 0.8568 (mmp) cc_final: 0.8202 (mmp)
REVERT: H   79 GLU cc_start: 0.0825 (OUTLIER) cc_final: -0.0880 (mm-30)
REVERT: D   92 TYR cc_start: 0.8051 (t80) cc_final: 0.7806 (t80)
REVERT: D  130 ARG cc_start: 0.8887 (tmm160) cc_final: 0.8651 (ttp80)
  outliers start: 29
  outliers final: 8
  residues processed: 191
  average time/residue: 0.1618
  time to fit residues: 41.4973
Evaluate side-chains
  114 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    4 GLU
Chi-restraints excluded: chain B residue   85 LYS
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  179 ARG
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue  177 PHE
Chi-restraints excluded: chain G residue   78 SER
Chi-restraints excluded: chain G residue   79 GLU
Chi-restraints excluded: chain H residue   79 GLU
Chi-restraints excluded: chain H residue   81 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:   20.0000
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:   20.0000
   chunk 55 optimal weight:    0.9980
   overall best weight:    3.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  16 GLN
B  53 HIS
** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 101 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5064 r_free = 0.5064 target = 0.159348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4867 r_free = 0.4867 target = 0.143333 restraints weight = 106477.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4893 r_free = 0.4893 target = 0.143957 restraints weight = 70338.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4872 r_free = 0.4872 target = 0.143988 restraints weight = 48975.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.144300 restraints weight = 44166.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.144297 restraints weight = 39791.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.4792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5206
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.077  14041  Z= 0.299
  Angle     :  0.905  11.845  19659  Z= 0.513
  Chirality :  0.049   0.325   2115
  Planarity :  0.007   0.057   1934
  Dihedral  : 25.467 152.486   3264
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 20.75
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  9.62 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 11.97 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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 (0.22), residues: 1185
  helix: -1.39 (0.16), residues: 867
  sheet:  None (None), residues: 0
  loop : -2.71 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.029   0.001   ARG C 136 
 TYR   0.026   0.003   TYR A  51 
 PHE   0.035   0.003   PHE G 157 
 TRP   0.018   0.002   TRP A 178 
 HIS   0.011   0.002   HIS A 158 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00585 /  0.30 (14041)
  covalent geometry    : angle       0.90456 /  0.51 (19659)
  hydrogen bonds       : bond        0.08003 /  8.81 (  858)
  hydrogen bonds       : angle       5.86330 /  7.49 ( 2377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 123
  time to evaluate  : 0.352 
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: A   13 ARG cc_start: 0.6776 (mmp-170) cc_final: 0.6454 (mmp80)
REVERT: A  177 PHE cc_start: 0.5009 (OUTLIER) cc_final: 0.3158 (t80)
REVERT: C  199 MET cc_start: -0.2230 (mtm) cc_final: -0.2480 (mmp)
REVERT: H   68 TYR cc_start: 0.9666 (t80) cc_final: 0.9391 (t80)
  outliers start: 38
  outliers final: 21
  residues processed: 152
  average time/residue: 0.1340
  time to fit residues: 28.5843
Evaluate side-chains
  113 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  179 ARG
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  175 SER
Chi-restraints excluded: chain A residue  177 PHE
Chi-restraints excluded: chain G residue   45 ILE
Chi-restraints excluded: chain G residue   78 SER
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain H residue  126 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  127 HIS
Chi-restraints excluded: chain D residue  137 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 123 optimal weight:    8.9990
   chunk 78 optimal weight:   10.0000
   chunk 74 optimal weight:   30.0000
   chunk 30 optimal weight:    0.9990
   chunk 4 optimal weight:   10.0000
   chunk 6 optimal weight:   50.0000
   chunk 50 optimal weight:    9.9990
   chunk 88 optimal weight:   20.0000
   chunk 14 optimal weight:   50.0000
   chunk 46 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9980
   overall best weight:    4.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 127 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 127 HIS
H 152 ASN
D 133 ASN
** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 174 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5036 r_free = 0.5036 target = 0.156974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4787 r_free = 0.4787 target = 0.137154 restraints weight = 107373.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.138022 restraints weight = 64056.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4850 r_free = 0.4850 target = 0.139076 restraints weight = 42703.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4858 r_free = 0.4858 target = 0.139675 restraints weight = 32479.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4866 r_free = 0.4866 target = 0.140034 restraints weight = 28110.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.4725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5714
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.106  14041  Z= 0.334
  Angle     :  0.964  15.288  19659  Z= 0.532
  Chirality :  0.054   0.356   2115
  Planarity :  0.007   0.075   1934
  Dihedral  : 25.592 153.082   3250
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 28.75
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  : 10.55 %
    Favored  : 89.28 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 16.62 %
    Favored  : 78.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.35 %

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: -2.71 (0.22), residues: 1185
  helix: -1.35 (0.16), residues: 878
  sheet:  None (None), residues: 0
  loop : -2.69 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG G  90 
 TYR   0.033   0.003   TYR A  51 
 PHE   0.027   0.004   PHE B 106 
 TRP   0.024   0.002   TRP A 178 
 HIS   0.025   0.003   HIS B 190 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00678 /  0.33 (14041)
  covalent geometry    : angle       0.96387 /  0.53 (19659)
  hydrogen bonds       : bond        0.08532 /  9.43 (  858)
  hydrogen bonds       : angle       6.03312 /  7.69 ( 2377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 102
  time to evaluate  : 0.359 
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: A  191 PHE cc_start: 0.5113 (OUTLIER) cc_final: 0.3639 (t80)
REVERT: G  199 MET cc_start: 0.1829 (ppp) cc_final: 0.1547 (ppp)
REVERT: C  199 MET cc_start: -0.1744 (mtm) cc_final: -0.2456 (mmt)
REVERT: D  124 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8376 (mp0)
REVERT: D  127 HIS cc_start: 0.9074 (OUTLIER) cc_final: 0.8780 (t-90)
  outliers start: 51
  outliers final: 30
  residues processed: 144
  average time/residue: 0.1148
  time to fit residues: 23.9089
Evaluate side-chains
  120 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 87
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue   92 TYR
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  179 ARG
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   63 ARG
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain G residue    8 VAL
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   65 MET
Chi-restraints excluded: chain G residue   71 ASP
Chi-restraints excluded: chain G residue   78 SER
Chi-restraints excluded: chain G residue  170 VAL
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain H residue  126 LEU
Chi-restraints excluded: chain D residue   45 ILE
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  127 HIS
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  175 SER
Chi-restraints excluded: chain D residue  199 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 8 optimal weight:   40.0000
   chunk 97 optimal weight:   30.0000
   chunk 77 optimal weight:    5.9990
   chunk 70 optimal weight:    6.9990
   chunk 81 optimal weight:   10.0000
   chunk 49 optimal weight:    0.6980
   chunk 129 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    1.6786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
G 167 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5060 r_free = 0.5060 target = 0.158922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4863 r_free = 0.4863 target = 0.143838 restraints weight = 107057.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4854 r_free = 0.4854 target = 0.144091 restraints weight = 70698.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4897 r_free = 0.4897 target = 0.145323 restraints weight = 49135.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4890 r_free = 0.4890 target = 0.145282 restraints weight = 35474.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4888 r_free = 0.4888 target = 0.145247 restraints weight = 28637.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.4803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4975
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14041  Z= 0.210
  Angle     :  0.812  14.246  19659  Z= 0.455
  Chirality :  0.047   0.324   2115
  Planarity :  0.006   0.057   1934
  Dihedral  : 25.499 152.272   3246
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 21.95
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.87 %
    Favored  : 90.04 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 18.10 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -2.27 (0.23), residues: 1185
  helix: -1.00 (0.16), residues: 888
  sheet:  None (None), residues: 0
  loop : -2.65 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  90 
 TYR   0.031   0.003   TYR A  51 
 PHE   0.022   0.002   PHE B  26 
 TRP   0.020   0.002   TRP A 178 
 HIS   0.008   0.001   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.21 (14041)
  covalent geometry    : angle       0.81151 /  0.45 (19659)
  hydrogen bonds       : bond        0.06763 /  7.42 (  858)
  hydrogen bonds       : angle       5.62327 /  7.15 ( 2377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 100
  time to evaluate  : 0.472 
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: B  101 GLN cc_start: 0.3568 (OUTLIER) cc_final: 0.2418 (tp-100)
REVERT: A  191 PHE cc_start: 0.4765 (t80) cc_final: 0.3416 (t80)
REVERT: G   38 MET cc_start: 0.7692 (OUTLIER) cc_final: 0.7456 (ptp)
REVERT: G  199 MET cc_start: 0.1911 (ppp) cc_final: 0.1664 (ppp)
  outliers start: 43
  outliers final: 23
  residues processed: 137
  average time/residue: 0.1146
  time to fit residues: 22.9293
Evaluate side-chains
  117 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  179 ARG
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain G residue    8 VAL
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   78 SER
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue  190 HIS
Chi-restraints excluded: chain H residue  126 LEU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  127 HIS
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  175 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 96 optimal weight:    0.4980
   chunk 111 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0270
   chunk 91 optimal weight:   50.0000
   chunk 7 optimal weight:   50.0000
   chunk 31 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   chunk 63 optimal weight:    7.9990
   chunk 117 optimal weight:    1.9990
   chunk 121 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    1.2842

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 174 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 = 0.5069 r_free = 0.5069 target = 0.159798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.141671 restraints weight = 106729.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.142610 restraints weight = 65558.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4890 r_free = 0.4890 target = 0.143475 restraints weight = 45944.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4909 r_free = 0.4909 target = 0.143933 restraints weight = 34743.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4907 r_free = 0.4907 target = 0.144014 restraints weight = 35174.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.4785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5417
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  14041  Z= 0.193
  Angle     :  0.775  11.845  19659  Z= 0.439
  Chirality :  0.046   0.326   2115
  Planarity :  0.005   0.056   1934
  Dihedral  : 25.474 151.879   3246
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 21.39
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.11 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 19.98 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.86 (0.23), residues: 1185
  helix: -0.70 (0.16), residues: 890
  sheet:  None (None), residues: 0
  loop : -2.53 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G  83 
 TYR   0.031   0.002   TYR A  51 
 PHE   0.027   0.002   PHE B  26 
 TRP   0.016   0.001   TRP A 178 
 HIS   0.010   0.001   HIS B 190 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.19 (14041)
  covalent geometry    : angle       0.77548 /  0.44 (19659)
  hydrogen bonds       : bond        0.06265 /  6.85 (  858)
  hydrogen bonds       : angle       5.43661 /  6.93 ( 2377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 102
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 GLN cc_start: 0.3495 (OUTLIER) cc_final: 0.2461 (tp-100)
REVERT: A  182 LEU cc_start: 0.2585 (OUTLIER) cc_final: 0.2177 (mt)
REVERT: A  191 PHE cc_start: 0.4691 (t80) cc_final: 0.3341 (t80)
REVERT: G   38 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7590 (tmm)
REVERT: D  127 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.8584 (t-90)
  outliers start: 35
  outliers final: 25
  residues processed: 129
  average time/residue: 0.1248
  time to fit residues: 23.4125
Evaluate side-chains
  124 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  179 ARG
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain G residue    8 VAL
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   38 MET
Chi-restraints excluded: chain G residue   71 ASP
Chi-restraints excluded: chain G residue   78 SER
Chi-restraints excluded: chain G residue   92 TYR
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  195 ILE
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue  190 HIS
Chi-restraints excluded: chain H residue  126 LEU
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  127 HIS
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  199 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 119 optimal weight:    0.9980
   chunk 85 optimal weight:    8.9990
   chunk 1 optimal weight:   50.0000
   chunk 16 optimal weight:    0.4980
   chunk 11 optimal weight:   20.0000
   chunk 115 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 103 optimal weight:    0.8980
   chunk 88 optimal weight:    9.9990
   chunk 59 optimal weight:    0.2980
   chunk 26 optimal weight:    3.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 101 GLN
** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 133 ASN
D 167 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5083 r_free = 0.5083 target = 0.161066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4867 r_free = 0.4867 target = 0.143173 restraints weight = 106789.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.4896 r_free = 0.4896 target = 0.143683 restraints weight = 65412.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4906 r_free = 0.4906 target = 0.144103 restraints weight = 42096.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4922 r_free = 0.4922 target = 0.144760 restraints weight = 33906.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4926 r_free = 0.4926 target = 0.144942 restraints weight = 29150.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.4811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5340
moved from start:          0.4054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.092  14041  Z= 0.175
  Angle     :  0.748  12.153  19659  Z= 0.423
  Chirality :  0.045   0.331   2115
  Planarity :  0.005   0.057   1934
  Dihedral  : 25.454 151.061   3246
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 18.47
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.03 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 22.16 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.52 (0.24), residues: 1185
  helix: -0.43 (0.17), residues: 887
  sheet:  None (None), residues: 0
  loop : -2.49 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  63 
 TYR   0.029   0.002   TYR A  51 
 PHE   0.038   0.002   PHE B  26 
 TRP   0.011   0.001   TRP A 178 
 HIS   0.006   0.001   HIS H 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.18 (14041)
  covalent geometry    : angle       0.74800 /  0.42 (19659)
  hydrogen bonds       : bond        0.05715 /  6.25 (  858)
  hydrogen bonds       : angle       5.21994 /  6.65 ( 2377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 105
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 GLN cc_start: 0.3530 (OUTLIER) cc_final: 0.2678 (tp40)
REVERT: A  182 LEU cc_start: 0.2389 (OUTLIER) cc_final: 0.1947 (mt)
REVERT: A  191 PHE cc_start: 0.4653 (t80) cc_final: 0.3263 (t80)
REVERT: G  122 MET cc_start: 0.4022 (tpt) cc_final: 0.3640 (tpt)
REVERT: G  174 HIS cc_start: -0.0174 (OUTLIER) cc_final: -0.1250 (t70)
REVERT: D  124 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7930 (pm20)
REVERT: D  127 HIS cc_start: 0.8907 (OUTLIER) cc_final: 0.8556 (t-90)
  outliers start: 37
  outliers final: 23
  residues processed: 135
  average time/residue: 0.1323
  time to fit residues: 25.1764
Evaluate side-chains
  124 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  179 ARG
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue  102 ARG
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   78 SER
Chi-restraints excluded: chain G residue   92 TYR
Chi-restraints excluded: chain G residue  174 HIS
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue  190 HIS
Chi-restraints excluded: chain H residue  126 LEU
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  124 GLU
Chi-restraints excluded: chain D residue  127 HIS
Chi-restraints excluded: chain D residue  137 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 111 optimal weight:   20.0000
   chunk 24 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 106 optimal weight:    9.9990
   chunk 82 optimal weight:    0.2980
   chunk 76 optimal weight:    7.9990
   chunk 89 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 78 optimal weight:   20.0000
   chunk 119 optimal weight:    4.9990
   overall best weight:    1.8186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 174 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 = 0.5069 r_free = 0.5069 target = 0.160052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4891 r_free = 0.4891 target = 0.145507 restraints weight = 105991.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4861 r_free = 0.4861 target = 0.145551 restraints weight = 71941.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.145948 restraints weight = 49038.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4880 r_free = 0.4880 target = 0.146065 restraints weight = 40903.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4883 r_free = 0.4883 target = 0.146158 restraints weight = 35732.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.4804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4957
moved from start:          0.4352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067  14041  Z= 0.195
  Angle     :  0.766  10.487  19659  Z= 0.432
  Chirality :  0.046   0.330   2115
  Planarity :  0.006   0.096   1934
  Dihedral  : 25.465 150.936   3246
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 21.55
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.37 %
    Favored  : 90.55 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 22.95 %
    Favored  : 72.80 %
  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: -1.46 (0.23), residues: 1185
  helix: -0.39 (0.17), residues: 891
  sheet:  None (None), residues: 0
  loop : -2.46 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  96 
 TYR   0.030   0.002   TYR A  51 
 PHE   0.026   0.002   PHE A  26 
 TRP   0.013   0.001   TRP A 178 
 HIS   0.005   0.001   HIS H 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00385 /  0.20 (14041)
  covalent geometry    : angle       0.76595 /  0.43 (19659)
  hydrogen bonds       : bond        0.06109 /  6.71 (  858)
  hydrogen bonds       : angle       5.24454 /  6.70 ( 2377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 100
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 GLN cc_start: 0.3554 (OUTLIER) cc_final: 0.2360 (tp40)
REVERT: A   13 ARG cc_start: 0.6677 (mmp-170) cc_final: 0.6441 (mmp80)
REVERT: A  182 LEU cc_start: 0.2405 (OUTLIER) cc_final: 0.1971 (mt)
REVERT: A  191 PHE cc_start: 0.4800 (t80) cc_final: 0.3437 (t80)
REVERT: G   84 ASP cc_start: 0.8882 (p0) cc_final: 0.8318 (t0)
REVERT: G  174 HIS cc_start: 0.0414 (OUTLIER) cc_final: -0.0980 (t70)
REVERT: D  127 HIS cc_start: 0.8390 (OUTLIER) cc_final: 0.8141 (t-90)
  outliers start: 43
  outliers final: 31
  residues processed: 136
  average time/residue: 0.1224
  time to fit residues: 24.4850
Evaluate side-chains
  129 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 94
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   92 TYR
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  179 ARG
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain G residue    8 VAL
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   78 SER
Chi-restraints excluded: chain G residue   92 TYR
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  170 VAL
Chi-restraints excluded: chain G residue  174 HIS
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue  190 HIS
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain H residue  126 LEU
Chi-restraints excluded: chain D residue   21 THR
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  127 HIS
Chi-restraints excluded: chain D residue  137 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 112 optimal weight:    2.9990
   chunk 104 optimal weight:   20.0000
   chunk 57 optimal weight:    4.9990
   chunk 14 optimal weight:   50.0000
   chunk 13 optimal weight:   20.0000
   chunk 115 optimal weight:    0.6980
   chunk 43 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0370
   chunk 107 optimal weight:    8.9990
   chunk 76 optimal weight:    7.9990
   chunk 90 optimal weight:    6.9990
   overall best weight:    2.7464

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5051 r_free = 0.5051 target = 0.158656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4834 r_free = 0.4834 target = 0.143141 restraints weight = 105488.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4841 r_free = 0.4841 target = 0.143386 restraints weight = 67491.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4842 r_free = 0.4842 target = 0.143956 restraints weight = 48560.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4859 r_free = 0.4859 target = 0.144244 restraints weight = 35448.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4856 r_free = 0.4856 target = 0.144205 restraints weight = 30944.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.4766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5096
moved from start:          0.4726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.095  14041  Z= 0.229
  Angle     :  0.809  11.479  19659  Z= 0.455
  Chirality :  0.048   0.326   2115
  Planarity :  0.006   0.060   1934
  Dihedral  : 25.563 150.834   3246
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 25.15
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.70 %
    Favored  : 90.21 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 23.05 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -1.61 (0.23), residues: 1185
  helix: -0.50 (0.16), residues: 887
  sheet:  None (None), residues: 0
  loop : -2.49 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  96 
 TYR   0.029   0.003   TYR A  51 
 PHE   0.026   0.002   PHE A  26 
 TRP   0.019   0.002   TRP A 178 
 HIS   0.008   0.002   HIS A  53 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00463 /  0.23 (14041)
  covalent geometry    : angle       0.80919 /  0.46 (19659)
  hydrogen bonds       : bond        0.06636 /  7.33 (  858)
  hydrogen bonds       : angle       5.47622 /  6.93 ( 2377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 96
  time to evaluate  : 0.432 
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: B  101 GLN cc_start: 0.3667 (OUTLIER) cc_final: 0.2316 (tp40)
REVERT: A  182 LEU cc_start: 0.2752 (OUTLIER) cc_final: 0.2285 (mt)
REVERT: A  191 PHE cc_start: 0.4905 (OUTLIER) cc_final: 0.3551 (t80)
REVERT: G   84 ASP cc_start: 0.8840 (p0) cc_final: 0.8272 (t0)
REVERT: G  174 HIS cc_start: 0.0435 (OUTLIER) cc_final: -0.1551 (t70)
REVERT: C   97 MET cc_start: 0.7634 (mmt) cc_final: 0.7231 (mmt)
  outliers start: 51
  outliers final: 38
  residues processed: 137
  average time/residue: 0.1120
  time to fit residues: 22.6025
Evaluate side-chains
  133 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 91
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue   92 TYR
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  147 ASP
Chi-restraints excluded: chain B residue  179 ARG
Chi-restraints excluded: chain B residue  189 PHE
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   53 HIS
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   71 ASP
Chi-restraints excluded: chain G residue   78 SER
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  170 VAL
Chi-restraints excluded: chain G residue  174 HIS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue  190 HIS
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain H residue  126 LEU
Chi-restraints excluded: chain D residue   21 THR
Chi-restraints excluded: chain D residue   71 ASP
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  195 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 15 optimal weight:   50.0000
   chunk 129 optimal weight:   10.0000
   chunk 28 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 23 optimal weight:    8.9990
   chunk 81 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 6 optimal weight:   50.0000
   chunk 60 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 174 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5077 r_free = 0.5077 target = 0.160601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.145329 restraints weight = 106071.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4877 r_free = 0.4877 target = 0.145896 restraints weight = 64179.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4895 r_free = 0.4895 target = 0.146212 restraints weight = 47449.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4901 r_free = 0.4901 target = 0.146528 restraints weight = 35436.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4899 r_free = 0.4899 target = 0.146497 restraints weight = 31080.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.4814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4979
moved from start:          0.4846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073  14041  Z= 0.171
  Angle     :  0.759  11.310  19659  Z= 0.426
  Chirality :  0.046   0.332   2115
  Planarity :  0.005   0.060   1934
  Dihedral  : 25.565 149.761   3246
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 21.15
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.35 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 24.93 %
    Favored  : 71.41 %
  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: -1.24 (0.23), residues: 1185
  helix: -0.21 (0.17), residues: 880
  sheet:  None (None), residues: 0
  loop : -2.38 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG H  98 
 TYR   0.025   0.002   TYR A  51 
 PHE   0.025   0.002   PHE A  26 
 TRP   0.013   0.001   TRP A 178 
 HIS   0.017   0.001   HIS D 127 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.17 (14041)
  covalent geometry    : angle       0.75897 /  0.43 (19659)
  hydrogen bonds       : bond        0.05757 /  6.31 (  858)
  hydrogen bonds       : angle       5.24625 /  6.68 ( 2377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 96
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 GLN cc_start: 0.3746 (OUTLIER) cc_final: 0.2917 (tp40)
REVERT: B  199 MET cc_start: 0.4862 (tmm) cc_final: 0.4595 (ppp)
REVERT: A   13 ARG cc_start: 0.6596 (mmp-170) cc_final: 0.6380 (mmp80)
REVERT: A  182 LEU cc_start: 0.2802 (OUTLIER) cc_final: 0.2351 (mt)
REVERT: A  191 PHE cc_start: 0.4858 (OUTLIER) cc_final: 0.3443 (t80)
REVERT: G   76 PHE cc_start: 0.7643 (m-80) cc_final: 0.6880 (m-10)
REVERT: G  174 HIS cc_start: 0.0363 (OUTLIER) cc_final: -0.1592 (t70)
REVERT: C   97 MET cc_start: 0.7534 (mmt) cc_final: 0.7162 (mmt)
REVERT: H   38 MET cc_start: 0.3836 (mtt) cc_final: 0.3619 (mtm)
  outliers start: 37
  outliers final: 29
  residues processed: 126
  average time/residue: 0.1096
  time to fit residues: 20.5250
Evaluate side-chains
  124 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 91
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  179 ARG
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   53 HIS
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   78 SER
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  170 VAL
Chi-restraints excluded: chain G residue  174 HIS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue  190 HIS
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain H residue  126 LEU
Chi-restraints excluded: chain D residue   21 THR
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  137 LEU
Chi-restraints excluded: chain D residue  195 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0170
   chunk 46 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 71 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 118 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0670
   chunk 22 optimal weight:    0.9980
   chunk 9 optimal weight:   50.0000
   overall best weight:    0.4556

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 133 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5087 r_free = 0.5087 target = 0.161496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4863 r_free = 0.4863 target = 0.143851 restraints weight = 106352.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4895 r_free = 0.4895 target = 0.144581 restraints weight = 64118.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.4922 r_free = 0.4922 target = 0.145625 restraints weight = 43390.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4931 r_free = 0.4931 target = 0.146065 restraints weight = 31243.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.4941 r_free = 0.4941 target = 0.146529 restraints weight = 25391.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.4823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5274
moved from start:          0.4993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  14041  Z= 0.162
  Angle     :  0.752  16.525  19659  Z= 0.416
  Chirality :  0.045   0.338   2115
  Planarity :  0.005   0.068   1934
  Dihedral  : 25.557 148.854   3246
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 19.67
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.02 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 25.32 %
    Favored  : 71.22 %
  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: -1.05 (0.24), residues: 1185
  helix: -0.05 (0.17), residues: 882
  sheet:  None (None), residues: 0
  loop : -2.42 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  98 
 TYR   0.027   0.002   TYR A  51 
 PHE   0.028   0.002   PHE G 188 
 TRP   0.011   0.001   TRP A 178 
 HIS   0.005   0.001   HIS H 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.16 (14041)
  covalent geometry    : angle       0.75178 /  0.42 (19659)
  hydrogen bonds       : bond        0.05492 /  6.06 (  858)
  hydrogen bonds       : angle       5.11362 /  6.53 ( 2377)

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

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

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2370 Ramachandran restraints generated.
    1185 Oldfield, 0 Emsley, 1185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 97
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  101 GLN cc_start: 0.3690 (OUTLIER) cc_final: 0.2973 (tp40)
REVERT: B  199 MET cc_start: 0.4603 (tmm) cc_final: 0.4395 (ppp)
REVERT: A   13 ARG cc_start: 0.6621 (mmp-170) cc_final: 0.6391 (mmp80)
REVERT: A  182 LEU cc_start: 0.2531 (OUTLIER) cc_final: 0.2053 (mt)
REVERT: A  191 PHE cc_start: 0.4719 (OUTLIER) cc_final: 0.3222 (t80)
REVERT: G  174 HIS cc_start: 0.0246 (OUTLIER) cc_final: -0.1437 (t70)
REVERT: C   97 MET cc_start: 0.7753 (mmt) cc_final: 0.7459 (mmt)
REVERT: D  127 HIS cc_start: 0.9119 (OUTLIER) cc_final: 0.8825 (t-90)
  outliers start: 35
  outliers final: 28
  residues processed: 122
  average time/residue: 0.1186
  time to fit residues: 21.3680
Evaluate side-chains
  124 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 91
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue   69 GLU
Chi-restraints excluded: chain B residue   88 LEU
Chi-restraints excluded: chain B residue  101 GLN
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  139 GLN
Chi-restraints excluded: chain B residue  179 ARG
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue   93 PHE
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain G residue    8 VAL
Chi-restraints excluded: chain G residue   21 THR
Chi-restraints excluded: chain G residue   49 THR
Chi-restraints excluded: chain G residue   78 SER
Chi-restraints excluded: chain G residue  105 LEU
Chi-restraints excluded: chain G residue  170 VAL
Chi-restraints excluded: chain G residue  174 HIS
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain C residue   68 TYR
Chi-restraints excluded: chain C residue  190 HIS
Chi-restraints excluded: chain H residue   19 LEU
Chi-restraints excluded: chain H residue  126 LEU
Chi-restraints excluded: chain D residue   21 THR
Chi-restraints excluded: chain D residue   75 LEU
Chi-restraints excluded: chain D residue  110 GLU
Chi-restraints excluded: chain D residue  127 HIS
Chi-restraints excluded: chain D residue  137 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 15 optimal weight:   50.0000
   chunk 116 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0670
   chunk 47 optimal weight:    0.9990
   chunk 98 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 96 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0370
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.6200

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5092 r_free = 0.5092 target = 0.162135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4864 r_free = 0.4864 target = 0.144546 restraints weight = 105751.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4898 r_free = 0.4898 target = 0.145185 restraints weight = 63316.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4918 r_free = 0.4918 target = 0.146199 restraints weight = 41151.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4934 r_free = 0.4934 target = 0.147169 restraints weight = 31261.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4939 r_free = 0.4939 target = 0.147432 restraints weight = 26090.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.4826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5221
moved from start:          0.5168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  14041  Z= 0.161
  Angle     :  0.767  19.986  19659  Z= 0.419
  Chirality :  0.045   0.340   2115
  Planarity :  0.005   0.066   1934
  Dihedral  : 25.552 148.118   3246
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 19.47
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.76 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 25.52 %
    Favored  : 71.12 %
  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: -0.89 (0.24), residues: 1185
  helix:  0.06 (0.17), residues: 889
  sheet:  None (None), residues: 0
  loop : -2.39 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 130 
 TYR   0.025   0.002   TYR A  51 
 PHE   0.033   0.002   PHE B  26 
 TRP   0.011   0.001   TRP A 178 
 HIS   0.005   0.001   HIS H 174 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.16 (14041)
  covalent geometry    : angle       0.76666 /  0.42 (19659)
  hydrogen bonds       : bond        0.05398 /  5.99 (  858)
  hydrogen bonds       : angle       5.03539 /  6.43 ( 2377)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3964.88 seconds
wall clock time: 68 minutes 29.26 seconds (4109.26 seconds total)