Starting phenix.real_space_refine
on Mon Jul 28 20:50:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rpw_24624/07_2025/7rpw_24624.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rpw_24624/07_2025/7rpw_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rpw_24624/07_2025/7rpw_24624.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rpw_24624/07_2025/7rpw_24624.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rpw_24624/07_2025/7rpw_24624.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rpw_24624/07_2025/7rpw_24624.cif"
  }
  resolution = 4.38
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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
          Unusual residues: {'AMP%rna2p': 1}
          Classifications: {'RNA_mixed': 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: 7.12, per 1000 atoms: 0.67
  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: 3.00
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  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: 3.96
  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: 3.93

  Time building geometry restraints manager: 3.45 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'  DA Z  22 "
       pdb=" O3'  DA Z  22 "
    ideal  model  delta    sigma   weight residual
    1.422  1.474 -0.052 3.00e-02 1.11e+03 3.02e+00
  bond pdb=" C3'  DA Z  13 "
       pdb=" O3'  DA Z  13 "
    ideal  model  delta    sigma   weight residual
    1.422  1.464 -0.042 3.00e-02 1.11e+03 1.92e+00
  bond pdb=" C   ILE E 285 "
       pdb=" O   ILE E 285 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.013 1.19e-02 7.06e+03 1.20e+00
  bond pdb=" C3'  DT Z  30 "
       pdb=" O3'  DT Z  30 "
    ideal  model  delta    sigma   weight residual
    1.422  1.455 -0.033 3.00e-02 1.11e+03 1.18e+00
  bond pdb=" C4'  DG Y   4 "
       pdb=" C3'  DG Y   4 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.021 2.00e-02 2.50e+03 1.07e+00
  ... (remaining 10886 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 14372
        1.25 -     2.50: 464
        2.50 -     3.75: 93
        3.75 -     5.00: 17
        5.00 -     6.25: 8
  Bond angle restraints: 14954
  Sorted by residual:
  angle pdb=" N   GLU E 366 "
        pdb=" CA  GLU E 366 "
        pdb=" C   GLU E 366 "
      ideal   model   delta    sigma   weight residual
     113.18  109.01    4.17 1.33e+00 5.65e-01 9.81e+00
  angle pdb=" N   ALA E 132 "
        pdb=" CA  ALA E 132 "
        pdb=" C   ALA E 132 "
      ideal   model   delta    sigma   weight residual
     111.02  114.02   -3.00 1.22e+00 6.72e-01 6.04e+00
  angle pdb=" C3'  DA Z  22 "
        pdb=" O3'  DA Z  22 "
        pdb=" P    DC Z  23 "
      ideal   model   delta    sigma   weight residual
     120.20  123.80   -3.60 1.50e+00 4.44e-01 5.77e+00
  angle pdb=" N   SER B  24 "
        pdb=" CA  SER B  24 "
        pdb=" C   SER B  24 "
      ideal   model   delta    sigma   weight residual
     114.09  110.45    3.64 1.55e+00 4.16e-01 5.51e+00
  angle pdb=" C   LYS C 243 "
        pdb=" N   VAL C 244 "
        pdb=" CA  VAL C 244 "
      ideal   model   delta    sigma   weight residual
     121.97  125.94   -3.97 1.80e+00 3.09e-01 4.86e+00
  ... (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: 1174
       0.035 -    0.069: 371
       0.069 -    0.104: 120
       0.104 -    0.139: 57
       0.139 -    0.173: 2
  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=" 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       2.35   -2.49   -0.14 2.00e-01 2.50e+01 5.13e-01
  chirality pdb=" CA  ILE E 231 "
            pdb=" N   ILE E 231 "
            pdb=" C   ILE E 231 "
            pdb=" CB  ILE E 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.77e-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:             0.540
  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:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     31.510
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.060
  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:3.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6815
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      :  0.003   0.052  10892  Z= 0.161
  Angle     :  0.570   6.255  14954  Z= 0.310
  Chirality :  0.042   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 : 18.05
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.003   0.001   TRP E  50 
 HIS   0.005   0.001   HIS B 157 
 PHE   0.018   0.001   PHE E  53 
 TYR   0.010   0.001   TYR C 196 
 ARG   0.004   0.000   ARG E 265 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21083 (  388)
  hydrogen bonds       : angle       9.19799 ( 1006)
  covalent geometry    : bond        0.00330 (10891)
  covalent geometry    : angle       0.57022 (14954)
  Misc. bond           : bond        0.05188 (    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  : 1.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 SER cc_start: 0.8094 (t) cc_final: 0.7567 (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: 0.7698 (tpt170)
REVERT: E  328 MET cc_start: 0.8601 (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: 0.2281
  time to fit residues: 76.4212
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  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    4.9990
   chunk 92 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 31 optimal weight:    9.9990
   chunk 62 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 95 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 58 optimal weight:    7.9990
   chunk 71 optimal weight:    0.0170
   chunk 110 optimal weight:    5.9990
   overall best weight:    1.7224

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

Flipped N/Q/H residues before XYZ refinement:
A  21 ASN
A 240 HIS
E 391 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.115733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.097980 restraints weight = 46510.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.098826 restraints weight = 36821.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.099402 restraints weight = 32178.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3943
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3943 r_free = 0.3943    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 = 0.3941 r_free = 0.3941    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6737
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10892  Z= 0.158
  Angle     :  0.651   6.184  14954  Z= 0.351
  Chirality :  0.047   0.265   1724
  Planarity :  0.004   0.035   1681
  Dihedral  : 22.055 175.421   1931
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 15.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.33 %
    Favored  : 89.58 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.78 %
    Favored  : 96.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.70 (0.24), residues: 1171
  helix: -0.49 (0.29), residues: 308
  sheet: -1.48 (0.31), residues: 309
  loop : -2.77 (0.24), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP E  50 
 HIS   0.004   0.001   HIS B 157 
 PHE   0.022   0.002   PHE E  53 
 TYR   0.017   0.002   TYR B  56 
 ARG   0.005   0.001   ARG E 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04665 (  388)
  hydrogen bonds       : angle       6.80778 ( 1006)
  covalent geometry    : bond        0.00344 (10891)
  covalent geometry    : angle       0.65074 (14954)
  Misc. bond           : bond        0.00034 (    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
  160 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 158
  time to evaluate  : 1.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 LEU cc_start: 0.7331 (mp) cc_final: 0.6576 (mp)
REVERT: A   80 SER cc_start: 0.8981 (t) cc_final: 0.8752 (p)
REVERT: B  136 LEU cc_start: 0.7372 (tp) cc_final: 0.6966 (tp)
REVERT: B  146 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6390 (tt0)
REVERT: B  216 GLU cc_start: 0.3787 (mm-30) cc_final: 0.3504 (mm-30)
REVERT: C    1 MET cc_start: 0.7737 (tpt) cc_final: 0.7183 (tpp)
REVERT: C   44 ILE cc_start: 0.8786 (mt) cc_final: 0.8538 (mm)
REVERT: C   80 VAL cc_start: 0.7499 (m) cc_final: 0.6022 (m)
REVERT: E    8 GLU cc_start: 0.7812 (tm-30) cc_final: 0.6809 (pt0)
REVERT: E   63 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7468 (mt-10)
REVERT: E  133 LEU cc_start: 0.7593 (mp) cc_final: 0.7257 (mt)
REVERT: E  164 ARG cc_start: 0.7949 (mtt180) cc_final: 0.7709 (mmt-90)
REVERT: E  360 TYR cc_start: 0.6149 (m-10) cc_final: 0.5813 (t80)
REVERT: E  372 LEU cc_start: 0.6391 (tp) cc_final: 0.6123 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 159
  average time/residue: 0.2524
  time to fit residues: 56.2080
Evaluate side-chains
  97 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 120 optimal weight:    7.9990
   chunk 109 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 66 optimal weight:    9.9990
   chunk 78 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 1 optimal weight:    6.9990
   chunk 117 optimal weight:    0.3980
   chunk 50 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    3.8788

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

Flipped N/Q/H residues before XYZ refinement:
B 204 ASN

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 = 0.110786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.092711 restraints weight = 47378.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.093547 restraints weight = 42474.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.094003 restraints weight = 39586.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3837
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3837 r_free = 0.3837    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3837 r_free = 0.3837    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3837
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10892  Z= 0.237
  Angle     :  0.736  10.062  14954  Z= 0.391
  Chirality :  0.048   0.206   1724
  Planarity :  0.005   0.037   1681
  Dihedral  : 22.244 172.206   1931
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 20.46
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 13.15 %
    Favored  : 86.76 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  5.81 %
    Favored  : 93.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.07 (0.23), residues: 1171
  helix: -0.70 (0.29), residues: 293
  sheet: -1.78 (0.30), residues: 315
  loop : -2.95 (0.23), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E  50 
 HIS   0.005   0.001   HIS B 157 
 PHE   0.020   0.003   PHE B 129 
 TYR   0.037   0.003   TYR C  59 
 ARG   0.006   0.001   ARG E 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06080 (  388)
  hydrogen bonds       : angle       6.80783 ( 1006)
  covalent geometry    : bond        0.00524 (10891)
  covalent geometry    : angle       0.73645 (14954)
  Misc. bond           : bond        0.00052 (    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
  122 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 119
  time to evaluate  : 1.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.9066 (t) cc_final: 0.8779 (p)
REVERT: B   47 PHE cc_start: 0.5961 (t80) cc_final: 0.5682 (t80)
REVERT: B  146 GLU cc_start: 0.6871 (mt-10) cc_final: 0.5914 (mt-10)
REVERT: B  216 GLU cc_start: 0.4789 (mm-30) cc_final: 0.4457 (mm-30)
REVERT: C   44 ILE cc_start: 0.8735 (mt) cc_final: 0.8488 (mm)
REVERT: C  150 THR cc_start: 0.8608 (p) cc_final: 0.8341 (t)
REVERT: E    8 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7049 (pt0)
REVERT: E   22 LEU cc_start: 0.7668 (pp) cc_final: 0.7437 (pp)
REVERT: E   63 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7478 (mt-10)
REVERT: E  123 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7531 (mm-30)
REVERT: E  133 LEU cc_start: 0.7863 (mp) cc_final: 0.7606 (mt)
REVERT: E  360 TYR cc_start: 0.6068 (m-10) cc_final: 0.5135 (t80)
REVERT: E  372 LEU cc_start: 0.6557 (tp) cc_final: 0.6225 (tp)
REVERT: E  381 TYR cc_start: 0.7351 (m-80) cc_final: 0.7112 (m-80)
  outliers start: 3
  outliers final: 1
  residues processed: 121
  average time/residue: 0.2232
  time to fit residues: 38.6569
Evaluate side-chains
  91 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 71 optimal weight:    4.9990
   chunk 9 optimal weight:   10.0000
   chunk 90 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 110 optimal weight:    9.9990
   overall best weight:    1.7384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.113558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.095771 restraints weight = 46448.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.096308 restraints weight = 40020.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.096908 restraints weight = 37724.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3901
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3901 r_free = 0.3901    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3901 r_free = 0.3901    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3901
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10892  Z= 0.147
  Angle     :  0.636   7.292  14954  Z= 0.338
  Chirality :  0.045   0.153   1724
  Planarity :  0.004   0.033   1681
  Dihedral  : 22.191 173.378   1931
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.08 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.82 (0.24), residues: 1171
  helix: -0.48 (0.30), residues: 295
  sheet: -1.67 (0.31), residues: 299
  loop : -2.77 (0.23), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E  50 
 HIS   0.004   0.001   HIS B 157 
 PHE   0.018   0.002   PHE E  53 
 TYR   0.025   0.001   TYR C  59 
 ARG   0.004   0.000   ARG E 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04151 (  388)
  hydrogen bonds       : angle       6.11021 ( 1006)
  covalent geometry    : bond        0.00330 (10891)
  covalent geometry    : angle       0.63640 (14954)
  Misc. bond           : bond        0.00033 (    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
  123 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.9071 (t) cc_final: 0.8791 (p)
REVERT: B    2 MET cc_start: 0.6071 (tmm) cc_final: 0.5757 (tmm)
REVERT: B   36 ARG cc_start: 0.7307 (mmt180) cc_final: 0.6412 (mpt180)
REVERT: B  216 GLU cc_start: 0.4723 (mm-30) cc_final: 0.4424 (mm-30)
REVERT: C   44 ILE cc_start: 0.8696 (mt) cc_final: 0.8428 (mm)
REVERT: C  150 THR cc_start: 0.8530 (p) cc_final: 0.8322 (t)
REVERT: E    8 GLU cc_start: 0.7812 (tm-30) cc_final: 0.6888 (pt0)
REVERT: E  123 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7401 (mm-30)
REVERT: E  133 LEU cc_start: 0.7551 (mp) cc_final: 0.7316 (mt)
REVERT: E  183 MET cc_start: 0.8147 (ptp) cc_final: 0.7883 (ptp)
REVERT: E  360 TYR cc_start: 0.5987 (m-10) cc_final: 0.5169 (t80)
REVERT: E  372 LEU cc_start: 0.6542 (tp) cc_final: 0.6257 (tp)
REVERT: E  381 TYR cc_start: 0.7422 (m-80) cc_final: 0.7200 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2714
  time to fit residues: 48.3003
Evaluate side-chains
  89 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 1.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   chunk 85 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 107 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 98 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 75 optimal weight:    8.9990
   chunk 17 optimal weight:    0.0670
   chunk 79 optimal weight:    8.9990
   overall best weight:    3.4124

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

Flipped N/Q/H residues before XYZ refinement:
E 392 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.108049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.089399 restraints weight = 46108.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.090370 restraints weight = 37155.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.090768 restraints weight = 34743.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3820
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3820 r_free = 0.3820    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3820 r_free = 0.3820    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3820
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6944
moved from start:          0.3700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10892  Z= 0.214
  Angle     :  0.716   8.823  14954  Z= 0.379
  Chirality :  0.047   0.167   1724
  Planarity :  0.004   0.036   1681
  Dihedral  : 22.229 172.346   1931
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 19.46
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 13.66 %
    Favored  : 86.25 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.39 %
    Favored  : 96.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.13 (0.23), residues: 1171
  helix: -0.77 (0.29), residues: 294
  sheet: -1.81 (0.30), residues: 314
  loop : -2.99 (0.23), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP E  50 
 HIS   0.010   0.002   HIS B 157 
 PHE   0.019   0.002   PHE E  53 
 TYR   0.033   0.002   TYR C  59 
 ARG   0.007   0.001   ARG B 210 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05634 (  388)
  hydrogen bonds       : angle       6.40474 ( 1006)
  covalent geometry    : bond        0.00477 (10891)
  covalent geometry    : angle       0.71618 (14954)
  Misc. bond           : bond        0.00035 (    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
  111 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 109
  time to evaluate  : 1.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.9111 (t) cc_final: 0.8776 (p)
REVERT: A  163 GLU cc_start: 0.8431 (tm-30) cc_final: 0.8222 (mp0)
REVERT: B  136 LEU cc_start: 0.7345 (tp) cc_final: 0.7080 (tp)
REVERT: B  216 GLU cc_start: 0.4817 (mm-30) cc_final: 0.4515 (mm-30)
REVERT: C   44 ILE cc_start: 0.8785 (mt) cc_final: 0.8509 (mm)
REVERT: E    8 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7053 (pt0)
REVERT: E  133 LEU cc_start: 0.7451 (mp) cc_final: 0.7103 (mt)
REVERT: E  360 TYR cc_start: 0.5006 (m-10) cc_final: 0.4384 (t80)
REVERT: E  372 LEU cc_start: 0.6192 (tp) cc_final: 0.5837 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 111
  average time/residue: 0.2871
  time to fit residues: 46.7904
Evaluate side-chains
  88 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 1.578 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 116 optimal weight:    6.9990
   chunk 98 optimal weight:    7.9990
   chunk 32 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   chunk 60 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 52 optimal weight:    9.9990
   chunk 23 optimal weight:    0.7980
   overall best weight:    2.7186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.109140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.090506 restraints weight = 45922.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.091270 restraints weight = 36869.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.091699 restraints weight = 34024.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3837
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3837 r_free = 0.3837    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 = 0.3837 r_free = 0.3837    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3837
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10892  Z= 0.181
  Angle     :  0.670   7.065  14954  Z= 0.354
  Chirality :  0.045   0.178   1724
  Planarity :  0.004   0.035   1681
  Dihedral  : 22.238 172.683   1931
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 17.43
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.30 %
    Favored  : 87.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.08 (0.23), residues: 1171
  helix: -0.77 (0.29), residues: 297
  sheet: -1.69 (0.30), residues: 308
  loop : -3.00 (0.23), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP E  50 
 HIS   0.008   0.002   HIS B 157 
 PHE   0.020   0.002   PHE C 228 
 TYR   0.029   0.002   TYR C  59 
 ARG   0.006   0.001   ARG E 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04784 (  388)
  hydrogen bonds       : angle       6.15988 ( 1006)
  covalent geometry    : bond        0.00406 (10891)
  covalent geometry    : angle       0.67029 (14954)
  Misc. bond           : bond        0.00024 (    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
  105 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 2.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.9153 (t) cc_final: 0.8813 (m)
REVERT: B   36 ARG cc_start: 0.7342 (mmt180) cc_final: 0.6428 (mmt-90)
REVERT: B  216 GLU cc_start: 0.4789 (mm-30) cc_final: 0.4482 (mm-30)
REVERT: C    1 MET cc_start: 0.8031 (tpp) cc_final: 0.7828 (tpp)
REVERT: C   44 ILE cc_start: 0.8658 (mt) cc_final: 0.8377 (mm)
REVERT: C   75 MET cc_start: 0.8720 (mmt) cc_final: 0.8190 (tpp)
REVERT: C  186 LEU cc_start: 0.8655 (tp) cc_final: 0.8448 (tp)
REVERT: E    8 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7204 (pt0)
REVERT: E   25 LEU cc_start: 0.9201 (mm) cc_final: 0.8934 (pp)
REVERT: E  360 TYR cc_start: 0.5311 (m-10) cc_final: 0.4343 (t80)
REVERT: E  372 LEU cc_start: 0.6210 (tp) cc_final: 0.5929 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.3094
  time to fit residues: 47.4319
Evaluate side-chains
  78 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 1.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 91 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 120 optimal weight:    3.9990
   chunk 75 optimal weight:    8.9990
   chunk 94 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   chunk 119 optimal weight:   20.0000
   chunk 78 optimal weight:    8.9990
   chunk 115 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    2.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.108721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.090294 restraints weight = 47140.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.090967 restraints weight = 42316.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.091361 restraints weight = 36689.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3829 r_free = 0.3829    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 = 0.3829 r_free = 0.3829    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
moved from start:          0.4015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10892  Z= 0.192
  Angle     :  0.682   8.082  14954  Z= 0.362
  Chirality :  0.046   0.152   1724
  Planarity :  0.004   0.035   1681
  Dihedral  : 22.253 172.699   1931
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 18.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 13.07 %
    Favored  : 86.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.23), residues: 1171
  helix: -0.80 (0.29), residues: 294
  sheet: -1.78 (0.30), residues: 310
  loop : -3.01 (0.23), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP E  50 
 HIS   0.007   0.002   HIS B 157 
 PHE   0.022   0.002   PHE C 228 
 TYR   0.034   0.002   TYR C  59 
 ARG   0.004   0.001   ARG E 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05098 (  388)
  hydrogen bonds       : angle       6.19513 ( 1006)
  covalent geometry    : bond        0.00428 (10891)
  covalent geometry    : angle       0.68183 (14954)
  Misc. bond           : bond        0.00025 (    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
  101 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 2.407 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.9094 (t) cc_final: 0.8741 (p)
REVERT: B   36 ARG cc_start: 0.7105 (mmt180) cc_final: 0.6720 (mmt90)
REVERT: B  121 GLN cc_start: 0.8430 (tm-30) cc_final: 0.7177 (tm-30)
REVERT: B  136 LEU cc_start: 0.7490 (tp) cc_final: 0.7203 (tp)
REVERT: B  216 GLU cc_start: 0.4631 (mm-30) cc_final: 0.4216 (mm-30)
REVERT: C    1 MET cc_start: 0.7653 (tpp) cc_final: 0.7411 (tpp)
REVERT: C   20 ARG cc_start: 0.7851 (mtt-85) cc_final: 0.7597 (mtt-85)
REVERT: C   44 ILE cc_start: 0.8793 (mt) cc_final: 0.8514 (mm)
REVERT: C   75 MET cc_start: 0.8680 (mmt) cc_final: 0.8147 (tpp)
REVERT: E    8 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7095 (pt0)
REVERT: E  251 MET cc_start: 0.5716 (tmm) cc_final: 0.5485 (tmm)
REVERT: E  360 TYR cc_start: 0.5054 (m-10) cc_final: 0.4093 (t80)
REVERT: E  372 LEU cc_start: 0.6241 (tp) cc_final: 0.5866 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.4359
  time to fit residues: 66.2524
Evaluate side-chains
  81 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 2.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 116 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 68 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9990
   chunk 92 optimal weight:    7.9990
   chunk 39 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 85 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   overall best weight:    1.9388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.112384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.094196 restraints weight = 46730.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.094567 restraints weight = 40759.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.095376 restraints weight = 34840.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3867
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3867 r_free = 0.3867    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3867 r_free = 0.3867    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3867
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6844
moved from start:          0.4174

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= 0.152
  Angle     :  0.636   7.213  14954  Z= 0.338
  Chirality :  0.045   0.176   1724
  Planarity :  0.003   0.034   1681
  Dihedral  : 22.203 173.113   1931
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.61 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.95 (0.23), residues: 1171
  helix: -0.66 (0.30), residues: 294
  sheet: -1.58 (0.31), residues: 297
  loop : -2.92 (0.23), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP E  50 
 HIS   0.005   0.001   HIS B 157 
 PHE   0.026   0.002   PHE C 228 
 TYR   0.028   0.001   TYR C  59 
 ARG   0.003   0.000   ARG E 140 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04132 (  388)
  hydrogen bonds       : angle       5.89457 ( 1006)
  covalent geometry    : bond        0.00343 (10891)
  covalent geometry    : angle       0.63577 (14954)
  Misc. bond           : bond        0.00017 (    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
  106 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 ILE cc_start: 0.8364 (mm) cc_final: 0.7842 (tp)
REVERT: A   80 SER cc_start: 0.9125 (t) cc_final: 0.8773 (m)
REVERT: A  229 MET cc_start: 0.7956 (mmm) cc_final: 0.7710 (mmm)
REVERT: B  121 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7758 (tm-30)
REVERT: B  216 GLU cc_start: 0.4470 (mm-30) cc_final: 0.4050 (mm-30)
REVERT: C    1 MET cc_start: 0.7440 (tpp) cc_final: 0.7176 (tpp)
REVERT: C   44 ILE cc_start: 0.8688 (mt) cc_final: 0.8389 (mm)
REVERT: C   75 MET cc_start: 0.8717 (mmt) cc_final: 0.8118 (tpp)
REVERT: E    8 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7039 (pt0)
REVERT: E  360 TYR cc_start: 0.5185 (m-10) cc_final: 0.4122 (t80)
REVERT: E  372 LEU cc_start: 0.6431 (tp) cc_final: 0.6122 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2228
  time to fit residues: 34.3210
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  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 90 optimal weight:    0.0770
   chunk 106 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 68 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 117 optimal weight:    7.9990
   chunk 2 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    2.2146

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.112171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.093839 restraints weight = 47818.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.094829 restraints weight = 39018.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.095539 restraints weight = 32284.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3869
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3869 r_free = 0.3869    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3869 r_free = 0.3869    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3869
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6851
moved from start:          0.4277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10892  Z= 0.162
  Angle     :  0.648   7.377  14954  Z= 0.343
  Chirality :  0.045   0.181   1724
  Planarity :  0.004   0.034   1681
  Dihedral  : 22.186 173.371   1931
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 16.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.38 %
    Favored  : 87.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.02 (0.23), residues: 1171
  helix: -0.70 (0.29), residues: 294
  sheet: -1.60 (0.30), residues: 304
  loop : -2.99 (0.23), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.004   TRP E  50 
 HIS   0.005   0.001   HIS B 157 
 PHE   0.023   0.002   PHE C 228 
 TYR   0.030   0.002   TYR C  59 
 ARG   0.003   0.000   ARG E 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04380 (  388)
  hydrogen bonds       : angle       5.87619 ( 1006)
  covalent geometry    : bond        0.00364 (10891)
  covalent geometry    : angle       0.64752 (14954)
  Misc. bond           : bond        0.00019 (    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
  104 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.9129 (t) cc_final: 0.8784 (m)
REVERT: B   36 ARG cc_start: 0.7318 (mmt180) cc_final: 0.6818 (mmt90)
REVERT: B  126 ASN cc_start: 0.7627 (t0) cc_final: 0.7423 (t0)
REVERT: B  216 GLU cc_start: 0.4521 (mm-30) cc_final: 0.4096 (mm-30)
REVERT: C    1 MET cc_start: 0.7449 (tpp) cc_final: 0.7024 (tpp)
REVERT: C   44 ILE cc_start: 0.8702 (mt) cc_final: 0.8430 (mm)
REVERT: C   75 MET cc_start: 0.8552 (mmt) cc_final: 0.7973 (tpp)
REVERT: E    8 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7042 (pt0)
REVERT: E  372 LEU cc_start: 0.6406 (tp) cc_final: 0.6106 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1974
  time to fit residues: 31.1674
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  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 113 optimal weight:    9.9990
   chunk 54 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 90 optimal weight:   30.0000
   chunk 105 optimal weight:    0.8980
   chunk 106 optimal weight:    5.9990
   chunk 117 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 120 optimal weight:   30.0000
   overall best weight:    2.9586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.110844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.092885 restraints weight = 47459.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.093492 restraints weight = 39555.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.094035 restraints weight = 36994.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3842
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3842 r_free = 0.3842    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3842 r_free = 0.3842    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3842
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6899
moved from start:          0.4395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10892  Z= 0.194
  Angle     :  0.694   7.805  14954  Z= 0.365
  Chirality :  0.046   0.189   1724
  Planarity :  0.004   0.035   1681
  Dihedral  : 22.223 173.227   1931
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 18.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 12.81 %
    Favored  : 87.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.23), residues: 1171
  helix: -0.84 (0.29), residues: 296
  sheet: -1.67 (0.30), residues: 300
  loop : -3.05 (0.23), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.003   TRP E  50 
 HIS   0.006   0.001   HIS B 157 
 PHE   0.026   0.002   PHE C 228 
 TYR   0.032   0.002   TYR C  59 
 ARG   0.004   0.001   ARG E 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04956 (  388)
  hydrogen bonds       : angle       6.06976 ( 1006)
  covalent geometry    : bond        0.00436 (10891)
  covalent geometry    : angle       0.69439 (14954)
  Misc. bond           : bond        0.00019 (    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
  105 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 SER cc_start: 0.9160 (t) cc_final: 0.8788 (p)
REVERT: B   36 ARG cc_start: 0.7201 (mmt180) cc_final: 0.6792 (mmt90)
REVERT: B  121 GLN cc_start: 0.8326 (tm-30) cc_final: 0.7645 (tm-30)
REVERT: B  216 GLU cc_start: 0.4621 (mm-30) cc_final: 0.4199 (mm-30)
REVERT: C    1 MET cc_start: 0.7157 (tpp) cc_final: 0.6770 (tpp)
REVERT: C   44 ILE cc_start: 0.8728 (mt) cc_final: 0.8456 (mm)
REVERT: C   75 MET cc_start: 0.8489 (mmt) cc_final: 0.7968 (tpp)
REVERT: E    8 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7135 (pt0)
REVERT: E  372 LEU cc_start: 0.6408 (tp) cc_final: 0.6015 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.2192
  time to fit residues: 35.0719
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  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 110 optimal weight:    5.9990
   chunk 79 optimal weight:    7.9990
   chunk 12 optimal weight:   20.0000
   chunk 116 optimal weight:    1.9990
   chunk 53 optimal weight:    7.9990
   chunk 48 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.7386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.113082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.095267 restraints weight = 46706.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.095746 restraints weight = 47433.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.096370 restraints weight = 37503.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3890
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3890 r_free = 0.3890    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3890 r_free = 0.3890    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.3890
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6812
moved from start:          0.4488

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= 0.144
  Angle     :  0.637   7.549  14954  Z= 0.336
  Chirality :  0.044   0.165   1724
  Planarity :  0.003   0.035   1681
  Dihedral  : 22.157 173.672   1931
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 14.74
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.61 %
    Favored  : 88.30 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.23), residues: 1171
  helix: -0.72 (0.29), residues: 301
  sheet: -1.52 (0.31), residues: 293
  loop : -3.02 (0.23), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP E  50 
 HIS   0.004   0.001   HIS B 157 
 PHE   0.019   0.001   PHE C 228 
 TYR   0.026   0.001   TYR C  59 
 ARG   0.003   0.000   ARG E 330 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03987 (  388)
  hydrogen bonds       : angle       5.71018 ( 1006)
  covalent geometry    : bond        0.00326 (10891)
  covalent geometry    : angle       0.63669 (14954)
  Misc. bond           : bond        0.00017 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 3681.36 seconds
wall clock time: 67 minutes 55.28 seconds (4075.28 seconds total)