Starting phenix.real_space_refine
on Fri Sep 11 17:41:05 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7rpw_24624/09_2026/7rpw_24624.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rpw_24624/09_2026/7rpw_24624.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7rpw_24624/09_2026/7rpw_24624.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7rpw_24624/09_2026/7rpw_24624.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rpw_24624/09_2026/7rpw_24624.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rpw_24624/09_2026/7rpw_24624.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rpw_24624/09_2026/7rpw_24624.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rpw_24624/09_2026/7rpw_24624.cif"
  }
  resolution = 4.38
  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=   0.001 sd=   0.101
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Mn      4      7.51       5
     P      63      5.49       5
     S      25      5.16       5
     C    6567      2.51       5
     N    1750      2.21       5
     O    2185      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10594
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 1953
          Classifications: {'peptide': 252}
          Link IDs: {'PTRANS': 8, 'TRANS': 243}
    Chain: "B"
      Number of atoms: 1922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1922
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 9, 'TRANS': 233}
    Chain: "C"
      Number of atoms: 1941
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 1941
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 5, 'TRANS': 239}
    Chain: "X"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 409
          Classifications: {'DNA': 20}
          Link IDs: {'rna3p': 19}
    Chain: "Y"
      Number of atoms: 229
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 229
          Classifications: {'DNA': 11}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 10}
    Chain: "Z"
      Number of atoms: 634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 634
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
    Chain: "E"
      Number of atoms: 3480
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 439, 3480
          Classifications: {'peptide': 439}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 13, 'TRANS': 425}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "X"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "Y"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 22
          Classifications: {'RNAv2': 1}
          Modifications used: {'rna2p': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.53, per 1000 atoms: 0.24
  Number of scatterers: 10594
  At special positions: 0
  Unit cell: (117, 106.5, 123, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      4     24.99
     S      25     16.00
     P      63     15.00
     O    2185      8.00
     N    1750      7.00
     C    6567      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 342.9 milliseconds
  

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2218

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 15 sheets defined
      28.1% alpha, 16.5% beta
      30 base pairs and 46 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 21
    Processing helix  chain 'A' and resid 74 through 80
      removed outlier: 3.712A  pdb=" N   ILE A  78 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 151
      removed outlier: 3.864A  pdb=" N   ASN A 144 " --> pdb=" O   GLU A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 165
    Processing helix  chain 'A' and resid 202 through 210
    Processing helix  chain 'B' and resid 10 through 20
    Processing helix  chain 'B' and resid 72 through 81
      removed outlier: 3.501A  pdb=" N   VAL B  76 " --> pdb=" O   LYS B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 147
      removed outlier: 4.131A  pdb=" N   LEU B 147 " --> pdb=" O   ILE B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 204
      removed outlier: 3.584A  pdb=" N   VAL B 202 " --> pdb=" O   GLY B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 207
      No H-bonds generated for 'chain 'B' and resid 205 through 207'
    Processing helix  chain 'C' and resid 9 through 20
      removed outlier: 3.705A  pdb=" N   ASP C  13 " --> pdb=" O   ARG C   9 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE C  14 " --> pdb=" O   VAL C  10 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   ILE C  15 " --> pdb=" O   LEU C  11 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   LEU C  18 " --> pdb=" O   ILE C  14 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ARG C  20 " --> pdb=" O   GLN C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 79
      removed outlier: 3.662A  pdb=" N   ILE C  77 " --> pdb=" O   TYR C  73 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU C  78 " --> pdb=" O   LEU C  74 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   LYS C  79 " --> pdb=" O   MET C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 135 through 147
      removed outlier: 4.070A  pdb=" N   LYS C 140 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   SER C 141 " --> pdb=" O   ASP C 137 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 12
      removed outlier: 4.706A  pdb=" N   ILE E   6 " --> pdb=" O   GLU E   2 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 18 through 33
      removed outlier: 3.804A  pdb=" N   THR E  23 " --> pdb=" O   ARG E  19 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   ALA E  24 " --> pdb=" O   LEU E  20 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 37 through 47
    Processing helix  chain 'E' and resid 51 through 55
      removed outlier: 3.522A  pdb=" N   LEU E  54 " --> pdb=" O   PRO E  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 75
    Processing helix  chain 'E' and resid 77 through 88
    Processing helix  chain 'E' and resid 90 through 97
      removed outlier: 3.840A  pdb=" N   ARG E  97 " --> pdb=" O   GLU E  93 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 133
      removed outlier: 4.304A  pdb=" N   LEU E 133 " --> pdb=" O   SER E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 138 through 153
      removed outlier: 4.557A  pdb=" N   LEU E 142 " --> pdb=" O   GLY E 138 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 160 through 168
      removed outlier: 4.067A  pdb=" N   ARG E 164 " --> pdb=" O   LYS E 160 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 175 through 189
      removed outlier: 3.514A  pdb=" N   VAL E 179 " --> pdb=" O   GLY E 175 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 192 through 204
      removed outlier: 4.544A  pdb=" N   ILE E 196 " --> pdb=" O   SER E 192 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ILE E 197 " --> pdb=" O   ALA E 193 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG E 204 " --> pdb=" O   ALA E 200 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 207 through 217
    Processing helix  chain 'E' and resid 246 through 252
    Processing helix  chain 'E' and resid 291 through 300
      removed outlier: 4.118A  pdb=" N   TYR E 295 " --> pdb=" O   ASP E 291 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   VAL E 296 " --> pdb=" O   VAL E 292 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   SER E 297 " --> pdb=" O   VAL E 293 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS E 298 " --> pdb=" O   ASP E 294 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 323 through 331
      removed outlier: 4.102A  pdb=" N   HIS E 329 " --> pdb=" O   GLN E 325 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ARG E 330 " --> pdb=" O   GLU E 326 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS E 331 " --> pdb=" O   LEU E 327 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 366 through 375
      removed outlier: 3.636A  pdb=" N   GLU E 373 " --> pdb=" O   ARG E 369 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER E 374 " --> pdb=" O   LYS E 370 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE E 375 " --> pdb=" O   LEU E 371 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 392 through 407
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
      removed outlier: 3.646A  pdb=" N   ILE A  89 " --> pdb=" O   TYR A   6 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   THR A  92 " --> pdb=" O   LYS A  99 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   LYS A  99 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLU C 175 " --> pdb=" O   LYS A 110 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   THR A 112 " --> pdb=" O   GLU C 173 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   GLU C 173 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52
      removed outlier: 4.116A  pdb=" N   ILE A  35 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   ARG A  38 " --> pdb=" O   ILE A  27 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   ILE A  27 " --> pdb=" O   ARG A  38 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   LEU A  40 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 9.028A  pdb=" N   SER A  25 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU A  70 " --> pdb=" O   ILE A  26 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   LEU A  28 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 138
      removed outlier: 3.622A  pdb=" N   VAL A 134 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 181
      removed outlier: 3.603A  pdb=" N   ALA A 179 " --> pdb=" O   ILE A 168 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.670A  pdb=" N   THR B  99 " --> pdb=" O   SER B  92 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 30
    Processing sheet with id=AA7, first strand: chain 'B' and resid 37 through 40
      removed outlier: 3.630A  pdb=" N   ASP B  49 " --> pdb=" O   ASP B 238 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   PHE B  51 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   TYR B 236 " --> pdb=" O   PHE B  51 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 189 through 190
      removed outlier: 3.694A  pdb=" N   SER B 189 " --> pdb=" O   LYS B 132 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LYS B 132 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 159
    Processing sheet with id=AB1, first strand: chain 'B' and resid 165 through 168
      removed outlier: 3.620A  pdb=" N   PHE B 165 " --> pdb=" O   VAL B 176 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   VAL C  97 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   ILE C  87 " --> pdb=" O   TYR C   5 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   TYR C   5 " --> pdb=" O   ILE C  87 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 26 through 29
      removed outlier: 4.749A  pdb=" N   VAL C  26 " --> pdb=" O   VAL C  37 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   VAL C  37 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU C  51 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE C  47 " --> pdb=" O   ALA C  38 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   LEU C  46 " --> pdb=" O   LEU C 239 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 130 through 131
      removed outlier: 3.516A  pdb=" N   PHE C 218 " --> pdb=" O   ILE C 130 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 162 through 165
      removed outlier: 3.890A  pdb=" N   SER C 192 " --> pdb=" O   GLY C 157 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'E' and resid 239 through 241
      removed outlier: 6.364A  pdb=" N   GLU E 239 " --> pdb=" O   LYS E 433 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 275 through 278
      removed outlier: 4.203A  pdb=" N   ILE E 307 " --> pdb=" O   ILE E 268 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ILE E 306 " --> pdb=" O   MET E 353 " (cutoff:3.500A)

    311 hydrogen bonds defined for protein.
    852 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      77 hydrogen bonds
      154 hydrogen bond angles
      0 basepair planarities
      30 basepair parallelities
      46 stacking parallelities
  Total time for adding SS restraints: 1.74

  Time building geometry restraints manager: 1.24 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2810
        1.33 -     1.45: 1960
        1.45 -     1.57: 5949
        1.57 -     1.69: 122
        1.69 -     1.81: 50
  Bond restraints: 10891
  Sorted by residual:
  bond pdb=" C3'  DC Z  26 "
       pdb=" C2'  DC Z  26 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.03e+01
  bond pdb=" C3'  DA Z  22 "
       pdb=" O3'  DA Z  22 "
    ideal  model  delta    sigma   weight residual
    1.435  1.474 -0.039 1.30e-02 5.92e+03 9.06e+00
  bond pdb=" C3'  DT Z  30 "
       pdb=" C2'  DT Z  30 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 8.00e-03 1.56e+04 8.23e+00
  bond pdb=" C4'  DG Y   4 "
       pdb=" C3'  DG Y   4 "
    ideal  model  delta    sigma   weight residual
    1.529  1.502  0.027 1.00e-02 1.00e+04 7.13e+00
  bond pdb=" C3'  DA X  16 "
       pdb=" C2'  DA X  16 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 8.00e-03 1.56e+04 6.39e+00
  ... (remaining 10886 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 14179
        1.25 -     2.50: 635
        2.50 -     3.75: 110
        3.75 -     5.00: 22
        5.00 -     6.25: 8
  Bond angle restraints: 14954
  Sorted by residual:
  angle pdb=" O4'  DG Y   5 "
        pdb=" C1'  DG Y   5 "
        pdb=" N9   DG Y   5 "
      ideal   model   delta    sigma   weight residual
     108.00  111.25   -3.25 7.00e-01 2.04e+00 2.16e+01
  angle pdb=" N3   DT Z  32 "
        pdb=" C4   DT Z  32 "
        pdb=" O4   DT Z  32 "
      ideal   model   delta    sigma   weight residual
     119.90  122.63   -2.73 6.00e-01 2.78e+00 2.07e+01
  angle pdb=" O4'  DG Y   4 "
        pdb=" C4'  DG Y   4 "
        pdb=" C3'  DG Y   4 "
      ideal   model   delta    sigma   weight residual
     106.00  103.33    2.67 6.00e-01 2.78e+00 1.97e+01
  angle pdb=" N3   DT Z  37 "
        pdb=" C4   DT Z  37 "
        pdb=" O4   DT Z  37 "
      ideal   model   delta    sigma   weight residual
     119.90  122.50   -2.60 6.00e-01 2.78e+00 1.87e+01
  angle pdb=" N3   DT X  10 "
        pdb=" C4   DT X  10 "
        pdb=" O4   DT X  10 "
      ideal   model   delta    sigma   weight residual
     119.90  122.48   -2.58 6.00e-01 2.78e+00 1.85e+01
  ... (remaining 14949 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.68: 6066
       34.68 -    69.36: 385
       69.36 -   104.04: 5
      104.04 -   138.72: 0
      138.72 -   173.39: 5
  Dihedral angle restraints: 6461
    sinusoidal: 3029
      harmonic: 3432
  Sorted by residual:
  dihedral pdb=" CA  SER E 139 "
           pdb=" C   SER E 139 "
           pdb=" N   ARG E 140 "
           pdb=" CA  ARG E 140 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.45  -24.55     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  LEU C 205 "
           pdb=" C   LEU C 205 "
           pdb=" N   SER C 206 "
           pdb=" CA  SER C 206 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.66   22.34     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  LEU C  11 "
           pdb=" C   LEU C  11 "
           pdb=" N   LYS C  12 "
           pdb=" CA  LYS C  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.44   20.56     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 6458 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1123
       0.035 -    0.069: 401
       0.069 -    0.104: 130
       0.104 -    0.139: 66
       0.139 -    0.173: 4
  Chirality restraints: 1724
  Sorted by residual:
  chirality pdb=" CB  VAL C 244 "
            pdb=" CA  VAL C 244 "
            pdb=" CG1 VAL C 244 "
            pdb=" CG2 VAL C 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.50e-01
  chirality pdb=" C3'  DA Z  22 "
            pdb=" C4'  DA Z  22 "
            pdb=" O3'  DA Z  22 "
            pdb=" C2'  DA Z  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.56   -0.17 2.00e-01 2.50e+01 7.37e-01
  chirality pdb=" P    DG Z  27 "
            pdb=" OP1  DG Z  27 "
            pdb=" OP2  DG Z  27 "
            pdb=" O5'  DG Z  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.49   -0.15 2.00e-01 2.50e+01 5.89e-01
  ... (remaining 1721 not shown)

  Planarity restraints: 1681
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  93 "    0.019 5.00e-02 4.00e+02   2.94e-02 1.39e+00
        pdb=" N   PRO C  94 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C  94 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  94 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E 226 "   -0.019 5.00e-02 4.00e+02   2.92e-02 1.37e+00
        pdb=" N   PRO E 227 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO E 227 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO E 227 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 121 "   -0.019 5.00e-02 4.00e+02   2.89e-02 1.33e+00
        pdb=" N   PRO B 122 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 122 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 122 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1678 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.38: 62
        2.38 -     3.01: 6110
        3.01 -     3.64: 17020
        3.64 -     4.27: 23587
        4.27 -     4.90: 36833
  Nonbonded interactions: 83612
  Sorted by model distance:
  nonbonded pdb=" O   GLY E  60 "
            pdb="MN    MN X 101 "
     model   vdw
     1.756 2.320
  nonbonded pdb=" OP1  DG X  22 "
            pdb="MN    MN E 701 "
     model   vdw
     1.835 2.320
  nonbonded pdb=" O3'  DG X  20 "
            pdb="MN    MN X 101 "
     model   vdw
     1.913 2.320
  nonbonded pdb=" O   LYS E 130 "
            pdb=" OG1 THR E 134 "
     model   vdw
     2.077 3.040
  nonbonded pdb=" OP1  DC X  21 "
            pdb="MN    MN X 102 "
     model   vdw
     2.146 2.320
  ... (remaining 83607 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     11.600
  Find NCS groups from input model:        0.160
  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:             0.000
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6776
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10892  Z= 0.284
  Angle     :  0.623   6.255  14954  Z= 0.435
  Chirality :  0.044   0.173   1724
  Planarity :  0.003   0.029   1681
  Dihedral  : 19.290 173.395   4243
  Min Nonbonded Distance : 1.756

Molprobity Statistics.
  All-atom Clashscore : 18.15
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.27 %
    Favored  : 88.64 %
  Rotamer:
    Outliers :  9.97 %
    Allowed  : 13.46 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.24), residues: 1171
  helix: -0.42 (0.30), residues: 300
  sheet: -1.68 (0.31), residues: 304
  loop : -2.82 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 265 
 TYR   0.010   0.001   TYR C 196 
 PHE   0.018   0.001   PHE E  53 
 TRP   0.003   0.001   TRP E  50 
 HIS   0.005   0.001   HIS B 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.28 (10891)
  covalent geometry    : angle       0.62347 /  0.44 (14954)
  hydrogen bonds       : bond        0.21083 / 14.20 (  388)
  hydrogen bonds       : angle       9.19799 /  6.35 ( 1006)
  Misc. bond           : bond        0.05188 /  2.73 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 103
    poor density    : 153
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 SER cc_start: 0.8093 (t) cc_final: 0.7566 (m)
REVERT: A   80 SER cc_start: 0.9022 (t) cc_final: 0.8779 (p)
REVERT: A  137 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8102 (t)
REVERT: B   21 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7684 (t0)
REVERT: B   89 LEU cc_start: 0.5247 (OUTLIER) cc_final: 0.4884 (tp)
REVERT: C   44 ILE cc_start: 0.9077 (mt) cc_final: 0.8816 (mm)
REVERT: C   75 MET cc_start: 0.7674 (OUTLIER) cc_final: 0.7341 (tpp)
REVERT: C  146 VAL cc_start: 0.7875 (t) cc_final: 0.6797 (t)
REVERT: E  123 GLU cc_start: 0.7720 (pp20) cc_final: 0.7429 (mp0)
REVERT: E  142 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7176 (mp)
REVERT: E  164 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7697 (tpt170)
REVERT: E  328 MET cc_start: 0.8600 (mtm) cc_final: 0.7994 (tmm)
REVERT: E  360 TYR cc_start: 0.4794 (OUTLIER) cc_final: 0.4463 (t80)
REVERT: E  372 LEU cc_start: 0.6464 (tp) cc_final: 0.6179 (tp)
  outliers start: 103
  outliers final: 40
  residues processed: 239
  average time/residue: 0.1014
  time to fit residues: 34.6970
Evaluate side-chains
  149 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 103
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    0.2980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:   20.0000
   overall best weight:    2.2586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  21 ASN
E 391 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.113549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.095764 restraints weight = 46733.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.096439 restraints weight = 38686.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.096981 restraints weight = 31994.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.098325 restraints weight = 26013.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.098363 restraints weight = 21684.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3960 r_free = 0.3960    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3959 r_free = 0.3959    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.3959
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6701
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10892  Z= 0.186
  Angle     :  0.727   7.776  14954  Z= 0.394
  Chirality :  0.051   0.346   1724
  Planarity :  0.005   0.050   1681
  Dihedral  : 22.185 174.012   1931
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 18.34
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.36 %
    Favored  : 88.56 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  3.78 %
    Favored  : 95.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.96 (0.23), residues: 1171
  helix: -0.70 (0.28), residues: 307
  sheet: -1.63 (0.30), residues: 315
  loop : -2.93 (0.23), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG E 145 
 TYR   0.021   0.002   TYR E 360 
 PHE   0.035   0.002   PHE B  60 
 TRP   0.027   0.004   TRP E  50 
 HIS   0.004   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00395 /  0.19 (10891)
  covalent geometry    : angle       0.72679 /  0.39 (14954)
  hydrogen bonds       : bond        0.06068 /  4.09 (  388)
  hydrogen bonds       : angle       7.50256 /  5.19 ( 1006)
  Misc. bond           : bond        0.00335 /  0.18 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 156
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 LEU cc_start: 0.7720 (mp) cc_final: 0.7285 (mp)
REVERT: A   80 SER cc_start: 0.9047 (t) cc_final: 0.8815 (p)
REVERT: B  146 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6567 (mt-10)
REVERT: B  216 GLU cc_start: 0.4330 (mm-30) cc_final: 0.3922 (mm-30)
REVERT: C    1 MET cc_start: 0.7562 (tpt) cc_final: 0.7203 (tpp)
REVERT: C   44 ILE cc_start: 0.8832 (mt) cc_final: 0.8603 (mm)
REVERT: C  146 VAL cc_start: 0.6973 (t) cc_final: 0.6546 (t)
REVERT: C  220 ASN cc_start: 0.7710 (m-40) cc_final: 0.7202 (m-40)
REVERT: E    8 GLU cc_start: 0.7725 (tm-30) cc_final: 0.6825 (pt0)
REVERT: E   63 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7446 (mt-10)
REVERT: E  133 LEU cc_start: 0.7626 (mp) cc_final: 0.7200 (mt)
REVERT: E  280 ARG cc_start: 0.6572 (tmt170) cc_final: 0.5895 (tpt90)
REVERT: E  328 MET cc_start: 0.8420 (mtm) cc_final: 0.8054 (tmm)
REVERT: E  372 LEU cc_start: 0.6347 (tp) cc_final: 0.6066 (tp)
  outliers start: 5
  outliers final: 1
  residues processed: 160
  average time/residue: 0.1135
  time to fit residues: 25.4534
Evaluate side-chains
  99 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 78 optimal weight:   30.0000
   chunk 116 optimal weight:   10.0000
   chunk 115 optimal weight:   40.0000
   chunk 101 optimal weight:    0.0770
   chunk 107 optimal weight:    0.0170
   chunk 73 optimal weight:   30.0000
   chunk 58 optimal weight:    9.9990
   chunk 37 optimal weight:    0.0020
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.7986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.117120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.099032 restraints weight = 46343.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.099757 restraints weight = 37450.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.100156 restraints weight = 36115.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.100728 restraints weight = 26650.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.101222 restraints weight = 23828.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3981 r_free = 0.3981    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3981 r_free = 0.3981    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (6 function evaluations)
r_final: 0.3981
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6679
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10892  Z= 0.148
  Angle     :  0.667   7.574  14954  Z= 0.360
  Chirality :  0.050   0.361   1724
  Planarity :  0.004   0.038   1681
  Dihedral  : 22.183 174.837   1931
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.39 %
    Favored  : 90.52 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.48 %
    Favored  : 96.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.97 (0.23), residues: 1171
  helix: -0.69 (0.28), residues: 310
  sheet: -1.67 (0.30), residues: 308
  loop : -2.94 (0.23), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  36 
 TYR   0.036   0.002   TYR C  59 
 PHE   0.020   0.002   PHE E  53 
 TRP   0.013   0.003   TRP E  50 
 HIS   0.003   0.001   HIS B 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.15 (10891)
  covalent geometry    : angle       0.66693 /  0.36 (14954)
  hydrogen bonds       : bond        0.04830 /  3.23 (  388)
  hydrogen bonds       : angle       6.93908 /  4.77 ( 1006)
  Misc. bond           : bond        0.00224 /  0.12 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 LEU cc_start: 0.7556 (mp) cc_final: 0.7075 (mp)
REVERT: A   80 SER cc_start: 0.9009 (t) cc_final: 0.8794 (p)
REVERT: A  163 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8444 (mp0)
REVERT: B   36 ARG cc_start: 0.7352 (mmt90) cc_final: 0.6945 (mmt90)
REVERT: B  126 ASN cc_start: 0.7227 (t0) cc_final: 0.7006 (t0)
REVERT: B  136 LEU cc_start: 0.7260 (tp) cc_final: 0.6860 (tp)
REVERT: B  146 GLU cc_start: 0.6213 (mt-10) cc_final: 0.5758 (tt0)
REVERT: B  216 GLU cc_start: 0.3777 (mm-30) cc_final: 0.3558 (mm-30)
REVERT: C    1 MET cc_start: 0.7566 (tpt) cc_final: 0.7148 (tpp)
REVERT: C   44 ILE cc_start: 0.8800 (mt) cc_final: 0.8552 (mm)
REVERT: C   75 MET cc_start: 0.7722 (mtt) cc_final: 0.7463 (tpp)
REVERT: C  146 VAL cc_start: 0.7082 (t) cc_final: 0.6808 (t)
REVERT: C  220 ASN cc_start: 0.8125 (m-40) cc_final: 0.7634 (m-40)
REVERT: E    8 GLU cc_start: 0.7687 (tm-30) cc_final: 0.6748 (pt0)
REVERT: E   63 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7396 (mt-10)
REVERT: E  133 LEU cc_start: 0.7840 (mp) cc_final: 0.7557 (mt)
REVERT: E  164 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7567 (tpt170)
REVERT: E  259 TYR cc_start: 0.8494 (t80) cc_final: 0.8050 (t80)
REVERT: E  328 MET cc_start: 0.8511 (mtm) cc_final: 0.8141 (tmm)
REVERT: E  372 LEU cc_start: 0.6279 (tp) cc_final: 0.6008 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1152
  time to fit residues: 21.6555
Evaluate side-chains
  98 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 75 optimal weight:   30.0000
   chunk 39 optimal weight:    0.0050
   chunk 120 optimal weight:   20.0000
   chunk 11 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0030
   chunk 22 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 83 optimal weight:   10.0000
   chunk 91 optimal weight:    0.7980
   chunk 31 optimal weight:    8.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    1.5608

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 221 GLN
** E 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.116085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.098106 restraints weight = 46861.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.099116 restraints weight = 40912.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.099686 restraints weight = 34802.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.099927 restraints weight = 26306.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.100806 restraints weight = 24152.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3986
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3986 r_free = 0.3986    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3986 r_free = 0.3986    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3986
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6679
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10892  Z= 0.147
  Angle     :  0.665   9.472  14954  Z= 0.354
  Chirality :  0.048   0.357   1724
  Planarity :  0.004   0.036   1681
  Dihedral  : 22.190 175.187   1931
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 15.46
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.93 %
    Favored  : 88.98 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.87 %
    Favored  : 95.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.93 (0.23), residues: 1171
  helix: -0.58 (0.28), residues: 307
  sheet: -1.64 (0.30), residues: 311
  loop : -2.96 (0.23), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 107 
 TYR   0.027   0.002   TYR C  59 
 PHE   0.019   0.002   PHE C 228 
 TRP   0.013   0.002   TRP E  50 
 HIS   0.004   0.001   HIS E 386 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.15 (10891)
  covalent geometry    : angle       0.66496 /  0.35 (14954)
  hydrogen bonds       : bond        0.04591 /  3.09 (  388)
  hydrogen bonds       : angle       6.78302 /  4.67 ( 1006)
  Misc. bond           : bond        0.00051 /  0.03 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.8952 (t) cc_final: 0.8744 (p)
REVERT: A  163 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8410 (mp0)
REVERT: B   36 ARG cc_start: 0.7210 (mmt90) cc_final: 0.6990 (mmt90)
REVERT: B  136 LEU cc_start: 0.7175 (tp) cc_final: 0.6940 (tp)
REVERT: B  146 GLU cc_start: 0.6440 (mt-10) cc_final: 0.5825 (tt0)
REVERT: B  216 GLU cc_start: 0.3897 (mm-30) cc_final: 0.3688 (mm-30)
REVERT: C   44 ILE cc_start: 0.8883 (mt) cc_final: 0.8637 (mm)
REVERT: C   65 PHE cc_start: 0.8480 (t80) cc_final: 0.8187 (t80)
REVERT: C   75 MET cc_start: 0.7694 (mtt) cc_final: 0.7491 (mmt)
REVERT: C  146 VAL cc_start: 0.7429 (t) cc_final: 0.7151 (t)
REVERT: E    8 GLU cc_start: 0.7666 (tm-30) cc_final: 0.6807 (pt0)
REVERT: E   63 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7405 (mt-10)
REVERT: E  133 LEU cc_start: 0.7632 (mp) cc_final: 0.7384 (mt)
REVERT: E  164 ARG cc_start: 0.7890 (mtt180) cc_final: 0.7680 (mmt-90)
REVERT: E  328 MET cc_start: 0.8542 (mtm) cc_final: 0.8165 (tmm)
REVERT: E  372 LEU cc_start: 0.6073 (tp) cc_final: 0.5799 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 124
  average time/residue: 0.1013
  time to fit residues: 17.8802
Evaluate side-chains
  97 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 101 optimal weight:   20.0000
   chunk 42 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 117 optimal weight:   20.0000
   chunk 73 optimal weight:   30.0000
   chunk 33 optimal weight:    7.9990
   chunk 75 optimal weight:   20.0000
   chunk 15 optimal weight:   10.0000
   chunk 9 optimal weight:    7.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 204 ASN
** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  21 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.107711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.089273 restraints weight = 46860.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.090356 restraints weight = 41440.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.090691 restraints weight = 37113.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.091608 restraints weight = 27710.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.091758 restraints weight = 24049.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3840 r_free = 0.3840    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3840 r_free = 0.3840    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (8 function evaluations)
r_final: 0.3840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.061  10892  Z= 0.309
  Angle     :  0.862  12.155  14954  Z= 0.451
  Chirality :  0.054   0.328   1724
  Planarity :  0.005   0.042   1681
  Dihedral  : 22.351 172.121   1931
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 24.61
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 14.86 %
    Favored  : 85.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  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: -3.36 (0.23), residues: 1171
  helix: -1.05 (0.28), residues: 294
  sheet: -1.76 (0.30), residues: 306
  loop : -3.21 (0.23), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 210 
 TYR   0.032   0.003   TYR B  56 
 PHE   0.025   0.003   PHE B  47 
 TRP   0.024   0.002   TRP E  50 
 HIS   0.008   0.002   HIS A 240 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00667 /  0.31 (10891)
  covalent geometry    : angle       0.86237 /  0.45 (14954)
  hydrogen bonds       : bond        0.07810 /  5.42 (  388)
  hydrogen bonds       : angle       7.23268 /  5.00 ( 1006)
  Misc. bond           : bond        0.00090 /  0.05 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 TYR cc_start: 0.6402 (t80) cc_final: 0.5756 (t80)
REVERT: A   80 SER cc_start: 0.9117 (t) cc_final: 0.8817 (p)
REVERT: A  163 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8530 (pp20)
REVERT: B  126 ASN cc_start: 0.6993 (t0) cc_final: 0.6776 (t0)
REVERT: B  146 GLU cc_start: 0.6309 (mt-10) cc_final: 0.5566 (mt-10)
REVERT: C   44 ILE cc_start: 0.8919 (mt) cc_final: 0.8710 (mm)
REVERT: C  213 TYR cc_start: 0.7932 (m-80) cc_final: 0.7447 (m-80)
REVERT: E    8 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7031 (pt0)
REVERT: E   63 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7584 (mt-10)
REVERT: E  123 GLU cc_start: 0.7321 (mp0) cc_final: 0.6905 (mp0)
REVERT: E  133 LEU cc_start: 0.7851 (mp) cc_final: 0.7600 (mt)
REVERT: E  328 MET cc_start: 0.8638 (mtm) cc_final: 0.8216 (tmm)
REVERT: E  372 LEU cc_start: 0.6197 (tp) cc_final: 0.5889 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1014
  time to fit residues: 15.7694
Evaluate side-chains
  83 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 47 optimal weight:    6.9990
   chunk 12 optimal weight:    8.9990
   chunk 31 optimal weight:    8.9990
   chunk 104 optimal weight:   20.0000
   chunk 107 optimal weight:    3.9990
   chunk 117 optimal weight:    0.0570
   chunk 83 optimal weight:    9.9990
   overall best weight:    2.2106

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 204 ASN
C 221 GLN
E 387 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.112889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.094705 restraints weight = 46754.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.095201 restraints weight = 37781.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.095724 restraints weight = 36164.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.096163 restraints weight = 26319.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.096702 restraints weight = 23999.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6809
moved from start:          0.3282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10892  Z= 0.169
  Angle     :  0.724  11.228  14954  Z= 0.382
  Chirality :  0.050   0.356   1724
  Planarity :  0.004   0.038   1681
  Dihedral  : 22.359 173.221   1931
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 18.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.19 %
    Favored  : 88.73 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.94 %
    Favored  : 97.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.12 (0.23), residues: 1171
  helix: -0.79 (0.29), residues: 296
  sheet: -1.73 (0.30), residues: 311
  loop : -3.02 (0.23), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 204 
 TYR   0.028   0.002   TYR C  59 
 PHE   0.025   0.002   PHE C 228 
 TRP   0.031   0.003   TRP E  50 
 HIS   0.005   0.001   HIS B 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.17 (10891)
  covalent geometry    : angle       0.72436 /  0.38 (14954)
  hydrogen bonds       : bond        0.04978 /  3.42 (  388)
  hydrogen bonds       : angle       6.72448 /  4.63 ( 1006)
  Misc. bond           : bond        0.00030 /  0.02 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 TYR cc_start: 0.6764 (t80) cc_final: 0.6169 (t80)
REVERT: A   80 SER cc_start: 0.9042 (t) cc_final: 0.8757 (p)
REVERT: A  229 MET cc_start: 0.6134 (mmm) cc_final: 0.5325 (mmm)
REVERT: B   36 ARG cc_start: 0.7194 (mmt90) cc_final: 0.6951 (mmt90)
REVERT: B  126 ASN cc_start: 0.6896 (t0) cc_final: 0.6648 (t0)
REVERT: B  146 GLU cc_start: 0.6352 (mt-10) cc_final: 0.5656 (mt-10)
REVERT: B  216 GLU cc_start: 0.4122 (mm-30) cc_final: 0.3878 (mm-30)
REVERT: C    1 MET cc_start: 0.7796 (tpp) cc_final: 0.7529 (tpp)
REVERT: C   44 ILE cc_start: 0.8804 (mt) cc_final: 0.8546 (mm)
REVERT: E    8 GLU cc_start: 0.7920 (tm-30) cc_final: 0.6900 (pt0)
REVERT: E   22 LEU cc_start: 0.7778 (pp) cc_final: 0.7496 (pp)
REVERT: E   25 LEU cc_start: 0.9182 (mm) cc_final: 0.8925 (pp)
REVERT: E   63 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7354 (mt-10)
REVERT: E  123 GLU cc_start: 0.7497 (mp0) cc_final: 0.6959 (mp0)
REVERT: E  133 LEU cc_start: 0.7963 (mp) cc_final: 0.7679 (mt)
REVERT: E  251 MET cc_start: 0.6572 (ttt) cc_final: 0.6050 (ttt)
REVERT: E  299 TYR cc_start: 0.8040 (m-10) cc_final: 0.7789 (m-80)
REVERT: E  328 MET cc_start: 0.8577 (mtm) cc_final: 0.8144 (tmm)
REVERT: E  372 LEU cc_start: 0.5919 (tp) cc_final: 0.5601 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0995
  time to fit residues: 16.6425
Evaluate side-chains
  90 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 85 optimal weight:    6.9990
   chunk 90 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 76 optimal weight:   40.0000
   chunk 31 optimal weight:    7.9990
   chunk 87 optimal weight:    7.9990
   chunk 118 optimal weight:   30.0000
   chunk 48 optimal weight:    2.9990
   chunk 115 optimal weight:    0.0020
   overall best weight:    4.3996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 221 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.110509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.092364 restraints weight = 47580.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.092999 restraints weight = 41420.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.093513 restraints weight = 35766.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.094272 restraints weight = 26578.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.094420 restraints weight = 23915.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6910
moved from start:          0.3455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  10892  Z= 0.248
  Angle     :  0.789   9.547  14954  Z= 0.415
  Chirality :  0.051   0.332   1724
  Planarity :  0.005   0.075   1681
  Dihedral  : 22.400 172.378   1931
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 22.20
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 14.18 %
    Favored  : 85.74 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.58 %
    Favored  : 96.32 %
  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: -3.38 (0.23), residues: 1171
  helix: -0.93 (0.29), residues: 288
  sheet: -1.88 (0.30), residues: 311
  loop : -3.21 (0.22), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 369 
 TYR   0.029   0.002   TYR C  59 
 PHE   0.026   0.003   PHE C 228 
 TRP   0.034   0.005   TRP E  50 
 HIS   0.016   0.002   HIS B 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00533 /  0.25 (10891)
  covalent geometry    : angle       0.78858 /  0.41 (14954)
  hydrogen bonds       : bond        0.06465 /  4.47 (  388)
  hydrogen bonds       : angle       6.96132 /  4.77 ( 1006)
  Misc. bond           : bond        0.00042 /  0.02 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 TYR cc_start: 0.5964 (t80) cc_final: 0.5153 (t80)
REVERT: A   80 SER cc_start: 0.9093 (t) cc_final: 0.8793 (p)
REVERT: A  229 MET cc_start: 0.7813 (mmm) cc_final: 0.6929 (mmm)
REVERT: B  126 ASN cc_start: 0.7138 (t0) cc_final: 0.6877 (t0)
REVERT: B  216 GLU cc_start: 0.4592 (mm-30) cc_final: 0.4307 (mm-30)
REVERT: C    1 MET cc_start: 0.7764 (tpp) cc_final: 0.7463 (tpp)
REVERT: C   44 ILE cc_start: 0.8727 (mt) cc_final: 0.8480 (mm)
REVERT: C   75 MET cc_start: 0.8537 (mmt) cc_final: 0.8183 (tpp)
REVERT: C  230 MET cc_start: 0.4757 (mmt) cc_final: 0.4116 (mpp)
REVERT: E   22 LEU cc_start: 0.7741 (pp) cc_final: 0.7512 (pp)
REVERT: E   25 LEU cc_start: 0.9228 (mm) cc_final: 0.8947 (pp)
REVERT: E   63 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7415 (mt-10)
REVERT: E  123 GLU cc_start: 0.7543 (mp0) cc_final: 0.7057 (mp0)
REVERT: E  133 LEU cc_start: 0.7926 (mp) cc_final: 0.7599 (mt)
REVERT: E  183 MET cc_start: 0.8478 (pmm) cc_final: 0.8154 (pmm)
REVERT: E  328 MET cc_start: 0.8393 (mtm) cc_final: 0.8045 (tmm)
REVERT: E  372 LEU cc_start: 0.5944 (tp) cc_final: 0.5616 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 0.0971
  time to fit residues: 14.7966
Evaluate side-chains
  82 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 94 optimal weight:    0.0980
   chunk 41 optimal weight:    0.7980
   chunk 106 optimal weight:    5.9990
   chunk 85 optimal weight:    0.7980
   chunk 84 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 8 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 118 optimal weight:   30.0000
   overall best weight:    1.7384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 221 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.113536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.095096 restraints weight = 46434.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.095519 restraints weight = 38560.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.096202 restraints weight = 33875.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.096952 restraints weight = 25587.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.097259 restraints weight = 23149.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6808
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10892  Z= 0.149
  Angle     :  0.700   8.659  14954  Z= 0.370
  Chirality :  0.050   0.362   1724
  Planarity :  0.004   0.068   1681
  Dihedral  : 22.386 172.877   1931
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 17.77
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.16 %
    Favored  : 89.75 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.06 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.04 (0.23), residues: 1171
  helix: -0.67 (0.30), residues: 284
  sheet: -1.63 (0.31), residues: 307
  loop : -2.99 (0.23), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  36 
 TYR   0.027   0.002   TYR C  59 
 PHE   0.022   0.002   PHE E  53 
 TRP   0.028   0.003   TRP E  50 
 HIS   0.005   0.001   HIS B 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.15 (10891)
  covalent geometry    : angle       0.70010 /  0.37 (14954)
  hydrogen bonds       : bond        0.04621 /  3.16 (  388)
  hydrogen bonds       : angle       6.49024 /  4.47 ( 1006)
  Misc. bond           : bond        0.00018 /  0.01 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 TYR cc_start: 0.6470 (t80) cc_final: 0.5589 (t80)
REVERT: A   80 SER cc_start: 0.9102 (t) cc_final: 0.8801 (p)
REVERT: A  229 MET cc_start: 0.7933 (mmm) cc_final: 0.7458 (mmm)
REVERT: B  126 ASN cc_start: 0.6965 (t0) cc_final: 0.6711 (t0)
REVERT: B  216 GLU cc_start: 0.4160 (mm-30) cc_final: 0.3911 (mm-30)
REVERT: C    1 MET cc_start: 0.7667 (tpp) cc_final: 0.7406 (tpp)
REVERT: C   44 ILE cc_start: 0.8807 (mt) cc_final: 0.8537 (mm)
REVERT: C   75 MET cc_start: 0.8383 (mmt) cc_final: 0.7959 (tpp)
REVERT: C  230 MET cc_start: 0.4290 (mmt) cc_final: 0.3880 (mmt)
REVERT: E    8 GLU cc_start: 0.7742 (tm-30) cc_final: 0.6608 (pt0)
REVERT: E   22 LEU cc_start: 0.7612 (pp) cc_final: 0.7412 (pp)
REVERT: E   25 LEU cc_start: 0.9209 (mm) cc_final: 0.8946 (pp)
REVERT: E   63 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7310 (mt-10)
REVERT: E  123 GLU cc_start: 0.7640 (mp0) cc_final: 0.7435 (mm-30)
REVERT: E  133 LEU cc_start: 0.7801 (mp) cc_final: 0.7506 (mt)
REVERT: E  183 MET cc_start: 0.8359 (pmm) cc_final: 0.8153 (pmm)
REVERT: E  294 ASP cc_start: 0.8460 (m-30) cc_final: 0.8212 (p0)
REVERT: E  328 MET cc_start: 0.8391 (mtm) cc_final: 0.8023 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0972
  time to fit residues: 15.4875
Evaluate side-chains
  88 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 65 optimal weight:    0.1980
   chunk 63 optimal weight:    0.5980
   chunk 77 optimal weight:   30.0000
   chunk 33 optimal weight:    0.9980
   chunk 121 optimal weight:   20.0000
   chunk 85 optimal weight:    5.9990
   chunk 79 optimal weight:    9.9990
   chunk 16 optimal weight:    7.9990
   chunk 58 optimal weight:    8.9990
   chunk 27 optimal weight:    0.9990
   chunk 115 optimal weight:    3.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 157 HIS
C 221 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.114571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.095758 restraints weight = 46478.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.096825 restraints weight = 35436.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.097486 restraints weight = 30217.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.097914 restraints weight = 24135.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.098205 restraints weight = 22872.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6788
moved from start:          0.3692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10892  Z= 0.139
  Angle     :  0.678   9.086  14954  Z= 0.357
  Chirality :  0.049   0.359   1724
  Planarity :  0.004   0.064   1681
  Dihedral  : 22.355 173.205   1931
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 17.24
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.76 %
    Favored  : 89.15 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.48 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.94 (0.24), residues: 1171
  helix: -0.70 (0.29), residues: 286
  sheet: -1.55 (0.31), residues: 304
  loop : -2.88 (0.24), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  20 
 TYR   0.032   0.002   TYR C  59 
 PHE   0.031   0.002   PHE C 228 
 TRP   0.026   0.003   TRP E  50 
 HIS   0.005   0.001   HIS B 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.14 (10891)
  covalent geometry    : angle       0.67753 /  0.36 (14954)
  hydrogen bonds       : bond        0.04401 /  3.00 (  388)
  hydrogen bonds       : angle       6.28969 /  4.35 ( 1006)
  Misc. bond           : bond        0.00026 /  0.01 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 TYR cc_start: 0.6313 (t80) cc_final: 0.5558 (t80)
REVERT: A   80 SER cc_start: 0.9023 (t) cc_final: 0.8757 (p)
REVERT: A  229 MET cc_start: 0.7947 (mmm) cc_final: 0.7275 (mmm)
REVERT: B  126 ASN cc_start: 0.6870 (t0) cc_final: 0.6595 (t0)
REVERT: B  216 GLU cc_start: 0.4095 (mm-30) cc_final: 0.3828 (mm-30)
REVERT: C    1 MET cc_start: 0.7678 (tpp) cc_final: 0.7321 (tpp)
REVERT: C   44 ILE cc_start: 0.8792 (mt) cc_final: 0.8535 (mm)
REVERT: C   75 MET cc_start: 0.8430 (mmt) cc_final: 0.7956 (tpp)
REVERT: C  230 MET cc_start: 0.4106 (mmt) cc_final: 0.3610 (mmt)
REVERT: E    8 GLU cc_start: 0.7791 (tm-30) cc_final: 0.6624 (pt0)
REVERT: E   25 LEU cc_start: 0.9225 (mm) cc_final: 0.8973 (pp)
REVERT: E   63 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7270 (mt-10)
REVERT: E  123 GLU cc_start: 0.7746 (mp0) cc_final: 0.7487 (mm-30)
REVERT: E  133 LEU cc_start: 0.7706 (mp) cc_final: 0.7401 (mt)
REVERT: E  183 MET cc_start: 0.8383 (pmm) cc_final: 0.8130 (pmm)
REVERT: E  328 MET cc_start: 0.8439 (mtm) cc_final: 0.8104 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0952
  time to fit residues: 15.0498
Evaluate side-chains
  82 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 108 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 111 optimal weight:   10.0000
   chunk 116 optimal weight:    9.9990
   chunk 92 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 68 optimal weight:    6.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    2.7784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 221 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.112755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.094547 restraints weight = 46411.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.094969 restraints weight = 39124.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.095572 restraints weight = 35038.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.096245 restraints weight = 26482.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.096451 restraints weight = 24097.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6828
moved from start:          0.3751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10892  Z= 0.179
  Angle     :  0.707   9.361  14954  Z= 0.372
  Chirality :  0.049   0.350   1724
  Planarity :  0.004   0.062   1681
  Dihedral  : 22.356 172.449   1931
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.38 %
    Favored  : 87.53 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.19 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.03 (0.24), residues: 1171
  helix: -0.75 (0.29), residues: 286
  sheet: -1.57 (0.31), residues: 309
  loop : -2.98 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  38 
 TYR   0.031   0.002   TYR C  59 
 PHE   0.032   0.002   PHE C 228 
 TRP   0.031   0.003   TRP E  50 
 HIS   0.009   0.001   HIS B 157 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00386 /  0.18 (10891)
  covalent geometry    : angle       0.70747 /  0.37 (14954)
  hydrogen bonds       : bond        0.05093 /  3.52 (  388)
  hydrogen bonds       : angle       6.37063 /  4.40 ( 1006)
  Misc. bond           : bond        0.00031 /  0.02 (    1)

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

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

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2342 Ramachandran restraints generated.
    1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 TYR cc_start: 0.5872 (t80) cc_final: 0.4974 (t80)
REVERT: A   80 SER cc_start: 0.9057 (t) cc_final: 0.8765 (p)
REVERT: A  229 MET cc_start: 0.7899 (mmm) cc_final: 0.7231 (mmm)
REVERT: B  126 ASN cc_start: 0.6982 (t0) cc_final: 0.6704 (t0)
REVERT: B  216 GLU cc_start: 0.4214 (mm-30) cc_final: 0.3951 (mm-30)
REVERT: C    1 MET cc_start: 0.7724 (tpp) cc_final: 0.7366 (tpp)
REVERT: C   44 ILE cc_start: 0.8805 (mt) cc_final: 0.8550 (mm)
REVERT: C   75 MET cc_start: 0.8603 (mmt) cc_final: 0.8186 (tpp)
REVERT: E    8 GLU cc_start: 0.7806 (tm-30) cc_final: 0.6662 (pt0)
REVERT: E   63 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7335 (mt-10)
REVERT: E  123 GLU cc_start: 0.7759 (mp0) cc_final: 0.7535 (mm-30)
REVERT: E  133 LEU cc_start: 0.7650 (mp) cc_final: 0.7339 (mt)
REVERT: E  183 MET cc_start: 0.8405 (pmm) cc_final: 0.8155 (pmm)
REVERT: E  328 MET cc_start: 0.8403 (mtm) cc_final: 0.8036 (tmm)
  outliers start: 1
  outliers final: 1
  residues processed: 103
  average time/residue: 0.1025
  time to fit residues: 15.6413
Evaluate side-chains
  84 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 64 optimal weight:    0.5980
   chunk 86 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0770
   chunk 43 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 92 optimal weight:    0.8980
   chunk 107 optimal weight:    0.0770
   chunk 52 optimal weight:    6.9990
   chunk 12 optimal weight:    0.3980
   overall best weight:    0.4096

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  21 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.116741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.098459 restraints weight = 45693.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.098568 restraints weight = 37330.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.099543 restraints weight = 32615.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.100069 restraints weight = 24586.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.100352 restraints weight = 23142.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10892  Z= 0.123
  Angle     :  0.663   8.806  14954  Z= 0.349
  Chirality :  0.048   0.376   1724
  Planarity :  0.004   0.061   1681
  Dihedral  : 22.303 173.800   1931
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.05 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.81 (0.24), residues: 1171
  helix: -0.55 (0.30), residues: 289
  sheet: -1.44 (0.32), residues: 304
  loop : -2.86 (0.23), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  20 
 TYR   0.021   0.001   TYR C  59 
 PHE   0.016   0.001   PHE C 228 
 TRP   0.024   0.003   TRP E  50 
 HIS   0.003   0.001   HIS A  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.12 (10891)
  covalent geometry    : angle       0.66287 /  0.35 (14954)
  hydrogen bonds       : bond        0.03753 /  2.53 (  388)
  hydrogen bonds       : angle       5.90935 /  4.09 ( 1006)
  Misc. bond           : bond        0.00001 /  0.00 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1591.32 seconds
wall clock time: 28 minutes 30.13 seconds (1710.13 seconds total)