Starting phenix.real_space_refine
on Sun Apr  5 03:33:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9p82_71362/04_2026/9p82_71362.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p82_71362/04_2026/9p82_71362.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p82_71362/04_2026/9p82_71362.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p82_71362/04_2026/9p82_71362.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p82_71362/04_2026/9p82_71362.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p82_71362/04_2026/9p82_71362.map"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.046
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
     P       3      5.49       5
     Mg      1      5.21       5
     S      52      5.16       5
     C    4917      2.51       5
     N    1323      2.21       5
     O    1403      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7699
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2320
          Classifications: {'peptide': 301}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 290}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 87
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 3, 'ASP:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 54
    Chain: "L"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
    Chain: "B"
      Number of atoms: 2491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2491
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 110
          Unresolved non-hydrogen angles: 135
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 6, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 85
    Chain: "C"
      Number of atoms: 364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 364
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 39
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 28
    Chain: "A"
      Number of atoms: 2433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2433
          Classifications: {'peptide': 349}
          Incomplete info: {'truncation_to_alanine': 102}
          Link IDs: {'PTRANS': 4, 'TRANS': 344}
          Unresolved non-hydrogen bonds: 367
          Unresolved non-hydrogen angles: 442
          Unresolved non-hydrogen dihedrals: 296
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLU:plan': 22, 'ASP:plan': 16, 'ARG:plan': 9, 'GLN:plan1': 7, 'PHE:plan': 2, 'ASN:plan1': 4}
          Unresolved non-hydrogen planarities: 233
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 33
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.51, per 1000 atoms: 0.20
  Number of scatterers: 7699
  At special positions: 0
  Unit cell: (104, 95.68, 123.968, 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)
     S      52     16.00
     P       3     15.00
     Mg      1     11.99
     O    1403      8.00
     N    1323      7.00
     C    4917      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 141 " - pdb=" SG  CYS R 224 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Conformation dependent library (CDL) restraints added in 303.7 milliseconds
  

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1980

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 9 sheets defined
      50.9% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'R' and resid 51 through 55
      removed outlier: 3.841A  pdb=" N   LEU R  54 " --> pdb=" O   SER R  51 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ASP R  55 " --> pdb=" O   SER R  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 51 through 55'
    Processing helix  chain 'R' and resid 59 through 90
    Processing helix  chain 'R' and resid 100 through 127
      removed outlier: 4.030A  pdb=" N   HIS R 104 " --> pdb=" O   THR R 100 " (cutoff:3.500A)
      Proline residue:  R 121  - end of helix
    Processing helix  chain 'R' and resid 136 through 172
    Processing helix  chain 'R' and resid 172 through 179
    Processing helix  chain 'R' and resid 181 through 200
      removed outlier: 3.504A  pdb=" N   ALA R 200 " --> pdb=" O   SER R 196 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 200 through 207
      removed outlier: 3.917A  pdb=" N   LEU R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   PHE R 205 " --> pdb=" O   VAL R 201 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   MET R 207 " --> pdb=" O   MET R 203 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 218 through 220
      No H-bonds generated for 'chain 'R' and resid 218 through 220'
    Processing helix  chain 'R' and resid 229 through 245
    Processing helix  chain 'R' and resid 245 through 273
    Processing helix  chain 'R' and resid 292 through 329
      removed outlier: 3.695A  pdb=" N   VAL R 309 " --> pdb=" O   LEU R 305 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
      removed outlier: 3.922A  pdb=" N   CYS R 327 " --> pdb=" O   ARG R 323 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 335 through 365
      removed outlier: 3.849A  pdb=" N   SER R 357 " --> pdb=" O   PHE R 353 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'C' and resid 11 through 24
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'A' and resid 7 through 32
    Processing helix  chain 'A' and resid 45 through 58
    Processing helix  chain 'A' and resid 62 through 68
    Processing helix  chain 'A' and resid 69 through 91
    Processing helix  chain 'A' and resid 98 through 113
      removed outlier: 4.272A  pdb=" N   ASP A 102 " --> pdb=" O   SER A  98 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ALA A 113 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 133
    Processing helix  chain 'A' and resid 133 through 141
    Processing helix  chain 'A' and resid 151 through 157
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.548A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.763A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.913A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 4.240A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 3.583A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 328 through 351
      removed outlier: 3.613A  pdb=" N   ASN A 346 " --> pdb=" O   VAL A 342 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ASN A 347 " --> pdb=" O   ILE A 343 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'R' and resid 209 through 211
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.525A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.919A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.246A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.998A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.255A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.725A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.950A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.275A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.537A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.619A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 191
      removed outlier: 6.321A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.233A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)

    461 hydrogen bonds defined for protein.
    1338 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.29

  Time building geometry restraints manager: 1.21 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: 1891
        1.33 -     1.45: 1592
        1.45 -     1.57: 4298
        1.57 -     1.69: 5
        1.69 -     1.81: 75
  Bond restraints: 7861
  Sorted by residual:
  bond pdb=" N   ILE L  12 "
       pdb=" CA  ILE L  12 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.10e-02 8.26e+03 9.58e+00
  bond pdb=" N   TYR L  11 "
       pdb=" CA  TYR L  11 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.034 1.31e-02 5.83e+03 6.83e+00
  bond pdb=" N   ILE B 273 "
       pdb=" CA  ILE B 273 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.27e-02 6.20e+03 6.76e+00
  bond pdb=" N   ILE B 270 "
       pdb=" CA  ILE B 270 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.25e-02 6.40e+03 5.70e+00
  bond pdb=" N   ASP B 267 "
       pdb=" CA  ASP B 267 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.28e-02 6.10e+03 5.64e+00
  ... (remaining 7856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.51: 10448
        1.51 -     3.02: 245
        3.02 -     4.53: 31
        4.53 -     6.04: 12
        6.04 -     7.55: 4
  Bond angle restraints: 10740
  Sorted by residual:
  angle pdb=" N   TYR L  11 "
        pdb=" CA  TYR L  11 "
        pdb=" C   TYR L  11 "
      ideal   model   delta    sigma   weight residual
     114.31  109.21    5.10 1.29e+00 6.01e-01 1.56e+01
  angle pdb=" C   LEU R 118 "
        pdb=" N   ALA R 119 "
        pdb=" CA  ALA R 119 "
      ideal   model   delta    sigma   weight residual
     122.42  115.74    6.68 1.77e+00 3.19e-01 1.42e+01
  angle pdb=" CA  CYS B 271 "
        pdb=" C   CYS B 271 "
        pdb=" O   CYS B 271 "
      ideal   model   delta    sigma   weight residual
     121.94  118.39    3.55 1.15e+00 7.56e-01 9.55e+00
  angle pdb=" C   TYR L  11 "
        pdb=" CA  TYR L  11 "
        pdb=" CB  TYR L  11 "
      ideal   model   delta    sigma   weight residual
     109.02  113.77   -4.75 1.68e+00 3.54e-01 8.01e+00
  angle pdb=" N   GLU A 239 "
        pdb=" CA  GLU A 239 "
        pdb=" C   GLU A 239 "
      ideal   model   delta    sigma   weight residual
     114.56  111.03    3.53 1.27e+00 6.20e-01 7.72e+00
  ... (remaining 10735 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.69: 4437
       32.69 -    65.37: 128
       65.37 -    98.06: 8
       98.06 -   130.75: 0
      130.75 -   163.43: 2
  Dihedral angle restraints: 4575
    sinusoidal: 1516
      harmonic: 3059
  Sorted by residual:
  dihedral pdb=" CB  CYS R 141 "
           pdb=" SG  CYS R 141 "
           pdb=" SG  CYS R 224 "
           pdb=" CB  CYS R 224 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -175.53   89.53     1      1.00e+01 1.00e-02 9.52e+01
  dihedral pdb=" C8  GTP A 402 "
           pdb=" C1' GTP A 402 "
           pdb=" N9  GTP A 402 "
           pdb=" O4' GTP A 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -58.84  163.43     1      2.00e+01 2.50e-03 4.70e+01
  dihedral pdb=" C5' GTP A 402 "
           pdb=" O5' GTP A 402 "
           pdb=" PA  GTP A 402 "
           pdb=" O3A GTP A 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -145.27 -145.46     1      2.00e+01 2.50e-03 4.38e+01
  ... (remaining 4572 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 989
       0.047 -    0.093: 226
       0.093 -    0.140: 61
       0.140 -    0.186: 2
       0.186 -    0.233: 2
  Chirality restraints: 1280
  Sorted by residual:
  chirality pdb=" CA  CYS B 271 "
            pdb=" N   CYS B 271 "
            pdb=" C   CYS B 271 "
            pdb=" CB  CYS B 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CA  ILE B 269 "
            pdb=" N   ILE B 269 "
            pdb=" C   ILE B 269 "
            pdb=" CB  ILE B 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CA  ILE B 270 "
            pdb=" N   ILE B 270 "
            pdb=" C   ILE B 270 "
            pdb=" CB  ILE B 270 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.47e-01
  ... (remaining 1277 not shown)

  Planarity restraints: 1352
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.040 5.00e-02 4.00e+02   6.10e-02 5.96e+00
        pdb=" N   PRO B 236 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 281 "   -0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO R 292 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO R 292 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO R 292 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 360 "    0.026 5.00e-02 4.00e+02   3.95e-02 2.49e+00
        pdb=" N   PRO R 361 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO R 361 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO R 361 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1349 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.82: 2186
        2.82 -     3.34: 7231
        3.34 -     3.86: 13217
        3.86 -     4.38: 14955
        4.38 -     4.90: 26184
  Nonbonded interactions: 63773
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 137 "
            pdb=" ND2 ASN A 141 "
     model   vdw
     2.294 3.120
  nonbonded pdb=" O   LYS B  89 "
            pdb=" NH1 ARG A  15 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" OE1 GLN R 238 "
            pdb=" OH  TYR R 328 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   THR R  78 "
            pdb=" OG1 THR R  82 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" N   SER A  44 "
            pdb=" O2B GTP A 402 "
     model   vdw
     2.323 3.120
  ... (remaining 63768 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.930
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.810
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
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   0.034   7862  Z= 0.174
  Angle     :  0.575   7.546  10742  Z= 0.340
  Chirality :  0.042   0.233   1280
  Planarity :  0.004   0.061   1352
  Dihedral  : 15.064 163.431   2592
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 15.46 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.26), residues: 1033
  helix:  2.46 (0.24), residues: 487
  sheet:  1.73 (0.41), residues: 156
  loop : -1.20 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R 182 
 TYR   0.012   0.001   TYR R 339 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7861)
  covalent geometry    : angle       0.57535 (10740)
  SS BOND              : bond        0.00218 (    1)
  SS BOND              : angle       0.51567 (    2)
  hydrogen bonds       : bond        0.12978 (  461)
  hydrogen bonds       : angle       5.27393 ( 1338)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.259 
Fit side-chains
REVERT: R  333 GLN cc_start: 0.7337 (mt0) cc_final: 0.7135 (mp10)
  outliers start: 6
  outliers final: 3
  residues processed: 109
  average time/residue: 0.6638
  time to fit residues: 75.9380
Evaluate side-chains
  102 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  146 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0770
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN
R 238 GLN
B 340 ASN
A 241 ASN
A 333 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.180008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.133218 restraints weight = 7990.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.76
r_work: 0.3516 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3420 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.0641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7862  Z= 0.115
  Angle     :  0.495   6.949  10742  Z= 0.264
  Chirality :  0.041   0.135   1280
  Planarity :  0.004   0.061   1352
  Dihedral  :  8.906 162.650   1139
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 13.68 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.77 (0.27), residues: 1033
  helix:  2.60 (0.24), residues: 486
  sheet:  1.46 (0.41), residues: 168
  loop : -0.95 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 182 
 TYR   0.013   0.001   TYR R 339 
 PHE   0.012   0.001   PHE B 151 
 TRP   0.017   0.001   TRP B 169 
 HIS   0.004   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 7861)
  covalent geometry    : angle       0.49529 (10740)
  SS BOND              : bond        0.00343 (    1)
  SS BOND              : angle       0.82055 (    2)
  hydrogen bonds       : bond        0.04802 (  461)
  hydrogen bonds       : angle       4.43441 ( 1338)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.300 
Fit side-chains
REVERT: R  333 GLN cc_start: 0.8074 (mt0) cc_final: 0.7841 (mp10)
REVERT: B   46 ARG cc_start: 0.7931 (mmp80) cc_final: 0.7265 (mmm-85)
REVERT: B  337 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7972 (mptp)
  outliers start: 21
  outliers final: 5
  residues processed: 114
  average time/residue: 0.6986
  time to fit residues: 83.5704
Evaluate side-chains
  107 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain R residue  325 MET
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain C residue   47 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 58 optimal weight:    0.0270
   chunk 7 optimal weight:    0.4980
   chunk 14 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   overall best weight:    0.6440

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
A 188 HIS
A 241 ASN
A 333 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.179973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.133296 restraints weight = 7955.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 1.76
r_work: 0.3520 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.0860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7862  Z= 0.110
  Angle     :  0.484   6.956  10742  Z= 0.257
  Chirality :  0.040   0.134   1280
  Planarity :  0.004   0.060   1352
  Dihedral  :  8.688 162.065   1134
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.05 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.26), residues: 1033
  helix:  2.69 (0.23), residues: 486
  sheet:  1.54 (0.43), residues: 155
  loop : -0.92 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 182 
 TYR   0.014   0.001   TYR R 339 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 7861)
  covalent geometry    : angle       0.48366 (10740)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       0.76746 (    2)
  hydrogen bonds       : bond        0.04653 (  461)
  hydrogen bonds       : angle       4.32176 ( 1338)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.338 
Fit side-chains
REVERT: R  333 GLN cc_start: 0.8091 (mt0) cc_final: 0.7861 (mp10)
REVERT: B   46 ARG cc_start: 0.7911 (mmp80) cc_final: 0.7261 (mmm-85)
REVERT: B  337 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7806 (mptp)
  outliers start: 16
  outliers final: 6
  residues processed: 116
  average time/residue: 0.6693
  time to fit residues: 81.5292
Evaluate side-chains
  108 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  153 ASP
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain C residue   47 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 57 optimal weight:    0.1980
   chunk 76 optimal weight:    0.1980
   chunk 8 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 41 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
A 188 HIS
A 333 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.178031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.130964 restraints weight = 8050.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 1.77
r_work: 0.3483 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3384 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.0956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7862  Z= 0.130
  Angle     :  0.520   8.025  10742  Z= 0.276
  Chirality :  0.042   0.140   1280
  Planarity :  0.004   0.060   1352
  Dihedral  :  9.059 165.121   1134
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 2.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 15.46 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.26), residues: 1033
  helix:  2.65 (0.23), residues: 486
  sheet:  1.42 (0.41), residues: 169
  loop : -0.95 (0.30), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 182 
 TYR   0.014   0.001   TYR R 339 
 PHE   0.016   0.001   PHE B 151 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.004   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7861)
  covalent geometry    : angle       0.51980 (10740)
  SS BOND              : bond        0.00295 (    1)
  SS BOND              : angle       0.89798 (    2)
  hydrogen bonds       : bond        0.05107 (  461)
  hydrogen bonds       : angle       4.36468 ( 1338)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.289 
Fit side-chains
REVERT: R  333 GLN cc_start: 0.8077 (mt0) cc_final: 0.7838 (mp-120)
REVERT: B   46 ARG cc_start: 0.7930 (mmp80) cc_final: 0.7261 (mmm-85)
REVERT: B  337 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7715 (mptp)
  outliers start: 17
  outliers final: 6
  residues processed: 109
  average time/residue: 0.6582
  time to fit residues: 75.3493
Evaluate side-chains
  106 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain C residue   47 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 92 optimal weight:    0.8980
   chunk 2 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 30 optimal weight:    5.9990
   chunk 83 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
A 171 GLN
A 188 HIS
A 244 HIS
A 333 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.176707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.129148 restraints weight = 7918.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 1.76
r_work: 0.3463 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3364 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7862  Z= 0.148
  Angle     :  0.551   8.575  10742  Z= 0.292
  Chirality :  0.042   0.149   1280
  Planarity :  0.004   0.061   1352
  Dihedral  :  9.380 166.791   1134
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.18 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.70 (0.26), residues: 1033
  helix:  2.56 (0.23), residues: 486
  sheet:  1.40 (0.41), residues: 169
  loop : -1.00 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 182 
 TYR   0.013   0.001   TYR R 339 
 PHE   0.018   0.002   PHE B 151 
 TRP   0.012   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 7861)
  covalent geometry    : angle       0.55040 (10740)
  SS BOND              : bond        0.00283 (    1)
  SS BOND              : angle       0.98940 (    2)
  hydrogen bonds       : bond        0.05459 (  461)
  hydrogen bonds       : angle       4.43915 ( 1338)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.283 
Fit side-chains
REVERT: R  333 GLN cc_start: 0.8102 (mt0) cc_final: 0.7879 (mp10)
REVERT: B   46 ARG cc_start: 0.7938 (mmp80) cc_final: 0.7271 (mmm-85)
REVERT: B  337 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7651 (mptp)
REVERT: A  245 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7665 (tm-30)
  outliers start: 19
  outliers final: 7
  residues processed: 112
  average time/residue: 0.6681
  time to fit residues: 78.7282
Evaluate side-chains
  106 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 97
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain A residue  245 GLU
Chi-restraints excluded: chain A residue  262 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 99 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 60 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 80 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN
R 238 GLN
B 266 HIS
B 340 ASN
A 171 GLN
A 188 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.173436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.132082 restraints weight = 7827.839|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 1.60
r_work: 0.3448 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   7862  Z= 0.230
  Angle     :  0.659  11.099  10742  Z= 0.350
  Chirality :  0.047   0.178   1280
  Planarity :  0.005   0.062   1352
  Dihedral  : 10.272 168.493   1134
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 14.91 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.26), residues: 1033
  helix:  2.25 (0.23), residues: 483
  sheet:  1.44 (0.40), residues: 168
  loop : -1.18 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 251 
 TYR   0.015   0.002   TYR B 111 
 PHE   0.026   0.002   PHE B 151 
 TRP   0.015   0.002   TRP B  82 
 HIS   0.008   0.002   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 7861)
  covalent geometry    : angle       0.65897 (10740)
  SS BOND              : bond        0.00275 (    1)
  SS BOND              : angle       1.34171 (    2)
  hydrogen bonds       : bond        0.06722 (  461)
  hydrogen bonds       : angle       4.69741 ( 1338)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.295 
Fit side-chains
REVERT: R  205 PHE cc_start: 0.7898 (m-80) cc_final: 0.7505 (m-10)
REVERT: R  333 GLN cc_start: 0.8222 (mt0) cc_final: 0.8008 (mp10)
REVERT: B   46 ARG cc_start: 0.7950 (mmp80) cc_final: 0.7295 (mmm-85)
REVERT: B  337 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7875 (mptp)
REVERT: A  241 ASN cc_start: 0.8056 (OUTLIER) cc_final: 0.7727 (t0)
  outliers start: 23
  outliers final: 8
  residues processed: 115
  average time/residue: 0.6682
  time to fit residues: 80.5074
Evaluate side-chains
  110 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  262 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 84 optimal weight:    0.8980
   chunk 98 optimal weight:    2.9990
   chunk 88 optimal weight:    7.9990
   chunk 28 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 30 optimal weight:    6.9990
   chunk 92 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
R 238 GLN
R 365 ASN
B 340 ASN
A 171 GLN
A 188 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.176877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.136553 restraints weight = 7900.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 1.79
r_work: 0.3493 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7862  Z= 0.137
  Angle     :  0.539   8.281  10742  Z= 0.288
  Chirality :  0.042   0.150   1280
  Planarity :  0.004   0.062   1352
  Dihedral  :  9.350 166.363   1134
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 15.87 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.26), residues: 1033
  helix:  2.37 (0.23), residues: 490
  sheet:  1.33 (0.41), residues: 169
  loop : -1.09 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 182 
 TYR   0.014   0.001   TYR R 339 
 PHE   0.016   0.001   PHE B 151 
 TRP   0.011   0.002   TRP B  82 
 HIS   0.004   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7861)
  covalent geometry    : angle       0.53928 (10740)
  SS BOND              : bond        0.00244 (    1)
  SS BOND              : angle       0.91999 (    2)
  hydrogen bonds       : bond        0.05349 (  461)
  hydrogen bonds       : angle       4.46346 ( 1338)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.276 
Fit side-chains
REVERT: R  205 PHE cc_start: 0.7888 (m-80) cc_final: 0.7508 (m-10)
REVERT: B  337 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7704 (mptp)
REVERT: A  241 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7634 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 107
  average time/residue: 0.7017
  time to fit residues: 78.6752
Evaluate side-chains
  109 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain C residue   38 MET
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  262 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 84 optimal weight:    6.9990
   chunk 98 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN
R 365 ASN
B 340 ASN
A 188 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.175200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.133893 restraints weight = 7896.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 1.77
r_work: 0.3482 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3383 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7862  Z= 0.166
  Angle     :  0.581   9.438  10742  Z= 0.308
  Chirality :  0.043   0.150   1280
  Planarity :  0.004   0.062   1352
  Dihedral  :  9.520 166.435   1134
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.60 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.26), residues: 1033
  helix:  2.39 (0.23), residues: 484
  sheet:  1.27 (0.41), residues: 169
  loop : -1.10 (0.29), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG R 182 
 TYR   0.014   0.002   TYR R 339 
 PHE   0.020   0.002   PHE B 151 
 TRP   0.013   0.002   TRP B  82 
 HIS   0.005   0.001   HIS R 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 7861)
  covalent geometry    : angle       0.58093 (10740)
  SS BOND              : bond        0.00288 (    1)
  SS BOND              : angle       1.01428 (    2)
  hydrogen bonds       : bond        0.05786 (  461)
  hydrogen bonds       : angle       4.52461 ( 1338)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.271 
Fit side-chains
REVERT: R  205 PHE cc_start: 0.7890 (m-80) cc_final: 0.7493 (m-10)
REVERT: B   46 ARG cc_start: 0.7914 (mmp80) cc_final: 0.7285 (mmm-85)
REVERT: B  337 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7809 (mptp)
REVERT: A  241 ASN cc_start: 0.7962 (OUTLIER) cc_final: 0.7673 (t0)
  outliers start: 19
  outliers final: 11
  residues processed: 109
  average time/residue: 0.7338
  time to fit residues: 83.6326
Evaluate side-chains
  110 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  262 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN
B 340 ASN
A 188 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.177863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.137707 restraints weight = 7954.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 1.78
r_work: 0.3514 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3415 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7862  Z= 0.120
  Angle     :  0.513   7.381  10742  Z= 0.273
  Chirality :  0.041   0.139   1280
  Planarity :  0.004   0.063   1352
  Dihedral  :  9.041 165.018   1134
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.42 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.27), residues: 1033
  helix:  2.49 (0.23), residues: 491
  sheet:  1.33 (0.41), residues: 168
  loop : -1.05 (0.30), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 182 
 TYR   0.015   0.001   TYR R 339 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.013   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A  57 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 7861)
  covalent geometry    : angle       0.51263 (10740)
  SS BOND              : bond        0.00263 (    1)
  SS BOND              : angle       0.78274 (    2)
  hydrogen bonds       : bond        0.04895 (  461)
  hydrogen bonds       : angle       4.35461 ( 1338)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.280 
Fit side-chains
REVERT: R  205 PHE cc_start: 0.7870 (m-80) cc_final: 0.7473 (m-10)
REVERT: B  337 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7664 (mptp)
REVERT: A  241 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7651 (t0)
  outliers start: 15
  outliers final: 9
  residues processed: 105
  average time/residue: 0.6985
  time to fit residues: 76.8979
Evaluate side-chains
  106 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  262 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 88 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 16 optimal weight:    0.2980
   chunk 69 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.178509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.138103 restraints weight = 7897.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3689 rms_B_bonded: 1.86
r_work: 0.3520 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3424 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7862  Z= 0.115
  Angle     :  0.503   7.201  10742  Z= 0.266
  Chirality :  0.041   0.135   1280
  Planarity :  0.004   0.062   1352
  Dihedral  :  8.909 163.545   1134
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 2.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 16.83 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.73 (0.27), residues: 1033
  helix:  2.65 (0.23), residues: 485
  sheet:  1.29 (0.41), residues: 168
  loop : -0.99 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 182 
 TYR   0.015   0.001   TYR R 339 
 PHE   0.013   0.001   PHE B 151 
 TRP   0.012   0.001   TRP B 169 
 HIS   0.003   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7861)
  covalent geometry    : angle       0.50257 (10740)
  SS BOND              : bond        0.00298 (    1)
  SS BOND              : angle       0.97552 (    2)
  hydrogen bonds       : bond        0.04701 (  461)
  hydrogen bonds       : angle       4.26847 ( 1338)

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

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

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2066 Ramachandran restraints generated.
    1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.290 
Fit side-chains
REVERT: R  205 PHE cc_start: 0.7862 (m-80) cc_final: 0.7513 (m-10)
REVERT: B  337 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.7679 (mptp)
REVERT: A  241 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7692 (t0)
  outliers start: 12
  outliers final: 9
  residues processed: 106
  average time/residue: 0.7245
  time to fit residues: 80.4500
Evaluate side-chains
  106 residues out of total 891 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  264 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  337 LYS
Chi-restraints excluded: chain C residue   47 GLU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain A residue  262 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 19 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 63 optimal weight:    7.9990
   chunk 93 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
R 126 ASN
R 365 ASN
B 340 ASN
A 188 HIS
A 333 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.177452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.132113 restraints weight = 7943.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.24
r_work: 0.3487 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3391 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7862  Z= 0.123
  Angle     :  0.516   7.607  10742  Z= 0.273
  Chirality :  0.041   0.137   1280
  Planarity :  0.004   0.062   1352
  Dihedral  :  9.038 164.564   1134
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.55 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.75 (0.26), residues: 1033
  helix:  2.65 (0.23), residues: 485
  sheet:  1.30 (0.41), residues: 169
  loop : -0.98 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG R 182 
 TYR   0.015   0.001   TYR R 339 
 PHE   0.014   0.001   PHE B 151 
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7861)
  covalent geometry    : angle       0.51555 (10740)
  SS BOND              : bond        0.00278 (    1)
  SS BOND              : angle       0.81808 (    2)
  hydrogen bonds       : bond        0.04875 (  461)
  hydrogen bonds       : angle       4.31961 ( 1338)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4002.39 seconds
wall clock time: 68 minutes 34.46 seconds (4114.46 seconds total)