Starting phenix.real_space_refine
on Sun Apr  5 01:18:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9p81_71361/04_2026/9p81_71361.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9p81_71361/04_2026/9p81_71361.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9p81_71361/04_2026/9p81_71361.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9p81_71361/04_2026/9p81_71361.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9p81_71361/04_2026/9p81_71361.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9p81_71361/04_2026/9p81_71361.map"
  }
  resolution = 2.6
  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=   0.039
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      45      5.16       5
     C    4288      2.51       5
     N    1149      2.21       5
     O    1198      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: 6684
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2400
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 169
          Unresolved non-hydrogen angles: 211
          Unresolved non-hydrogen dihedrals: 127
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 12, 'GLN:plan1': 6, 'ARG:plan': 7, 'ASN:plan1': 4}
          Unresolved non-hydrogen planarities: 131
    Chain: "C"
      Number of atoms: 362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 362
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 23
    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: "R"
      Number of atoms: 2264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2264
          Classifications: {'peptide': 297}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 286}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 91
          Unresolved non-hydrogen angles: 112
          Unresolved non-hydrogen dihedrals: 70
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 2, 'GLN:plan1': 3}
          Unresolved non-hydrogen planarities: 66
    Chain: "A"
      Number of atoms: 1567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1567
          Classifications: {'peptide': 221}
          Incomplete info: {'truncation_to_alanine': 62}
          Link IDs: {'PTRANS': 2, 'TRANS': 218}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 215
          Unresolved non-hydrogen angles: 260
          Unresolved non-hydrogen dihedrals: 172
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 10, 'ARG:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 2}
          Unresolved non-hydrogen planarities: 124
    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: 1.54, per 1000 atoms: 0.23
  Number of scatterers: 6684
  At special positions: 0
  Unit cell: (84.864, 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      45     16.00
     P       3     15.00
     Mg      1     11.99
     O    1198      8.00
     N    1149      7.00
     C    4288      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: 0.72
  Conformation dependent library (CDL) restraints added in 278.0 milliseconds
  

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1724

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 9 sheets defined
      48.0% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'C' and resid 10 through 24
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.520A  pdb=" N   ALA C  33 " --> pdb=" O   LYS C  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 51 through 55
      removed outlier: 3.541A  pdb=" N   ASP R  55 " --> pdb=" O   SER R  52 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 90
      removed outlier: 3.501A  pdb=" N   ARG R  90 " --> pdb=" O   PHE R  86 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 100 through 118
      removed outlier: 3.941A  pdb=" N   HIS R 104 " --> pdb=" O   THR R 100 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 119 through 127
    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
    Processing helix  chain 'R' and resid 202 through 207
      removed outlier: 3.811A  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 274
    Processing helix  chain 'R' and resid 293 through 327
      Proline residue:  R 318  - end of helix
      removed outlier: 3.925A  pdb=" N   CYS R 327 " --> pdb=" O   ARG R 323 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 330 through 334
    Processing helix  chain 'R' and resid 335 through 364
      removed outlier: 4.054A  pdb=" N   MET R 347 " --> pdb=" O   HIS R 343 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   SER R 357 " --> pdb=" O   PHE R 353 " (cutoff:3.500A)
      Proline residue:  R 361  - end of helix
    Processing helix  chain 'A' and resid 7 through 31
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.553A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.842A  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: 3.877A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 279
      removed outlier: 3.605A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.792A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.673A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.026A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.629A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.517A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.936A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.331A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.518A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.547A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'R' and resid 209 through 211
    Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 191
      removed outlier: 3.733A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.985A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)

    401 hydrogen bonds defined for protein.
    1152 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: 0.98

  Time building geometry restraints manager: 0.93 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: 1703
        1.33 -     1.45: 1334
        1.45 -     1.57: 3721
        1.57 -     1.69: 5
        1.69 -     1.81: 64
  Bond restraints: 6827
  Sorted by residual:
  bond pdb=" N   ILE L  12 "
       pdb=" CA  ILE L  12 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.035 1.24e-02 6.50e+03 8.17e+00
  bond pdb=" N   ILE A 278 "
       pdb=" CA  ILE A 278 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.26e-02 6.30e+03 7.64e+00
  bond pdb=" N   LYS B  57 "
       pdb=" CA  LYS B  57 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.23e-02 6.61e+03 7.59e+00
  bond pdb=" N   HIS B 266 "
       pdb=" CA  HIS B 266 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.21e-02 6.83e+03 7.45e+00
  bond pdb=" N   ILE B 273 "
       pdb=" CA  ILE B 273 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.20e-02 6.94e+03 7.04e+00
  ... (remaining 6822 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 9007
        1.47 -     2.94: 259
        2.94 -     4.41: 46
        4.41 -     5.88: 7
        5.88 -     7.35: 4
  Bond angle restraints: 9323
  Sorted by residual:
  angle pdb=" CA  ARG B 304 "
        pdb=" C   ARG B 304 "
        pdb=" O   ARG B 304 "
      ideal   model   delta    sigma   weight residual
     121.87  117.93    3.94 1.16e+00 7.43e-01 1.15e+01
  angle pdb=" CA  SER B 265 "
        pdb=" C   SER B 265 "
        pdb=" O   SER B 265 "
      ideal   model   delta    sigma   weight residual
     121.45  118.07    3.38 1.07e+00 8.73e-01 9.98e+00
  angle pdb=" N   GLU A 276 "
        pdb=" CA  GLU A 276 "
        pdb=" C   GLU A 276 "
      ideal   model   delta    sigma   weight residual
     113.15  109.40    3.75 1.19e+00 7.06e-01 9.92e+00
  angle pdb=" C   TYR B  59 "
        pdb=" CA  TYR B  59 "
        pdb=" CB  TYR B  59 "
      ideal   model   delta    sigma   weight residual
     109.07  114.26   -5.19 1.68e+00 3.54e-01 9.55e+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  110.77    3.79 1.27e+00 6.20e-01 8.88e+00
  ... (remaining 9318 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.46: 3852
       33.46 -    66.92: 97
       66.92 -   100.38: 5
      100.38 -   133.83: 0
      133.83 -   167.29: 2
  Dihedral angle restraints: 3956
    sinusoidal: 1299
      harmonic: 2657
  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 -175.20   89.20     1      1.00e+01 1.00e-02 9.47e+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  -62.70  167.29     1      2.00e+01 2.50e-03 4.74e+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 -126.59 -164.14     1      2.00e+01 2.50e-03 4.71e+01
  ... (remaining 3953 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 807
       0.041 -    0.083: 214
       0.083 -    0.124: 84
       0.124 -    0.165: 8
       0.165 -    0.207: 2
  Chirality restraints: 1115
  Sorted by residual:
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.07e+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    2.61   -0.18 2.00e-01 2.50e+01 8.16e-01
  chirality pdb=" CA  LEU A 273 "
            pdb=" N   LEU A 273 "
            pdb=" C   LEU A 273 "
            pdb=" CB  LEU A 273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.17e-01
  ... (remaining 1112 not shown)

  Planarity restraints: 1162
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 304 "   -0.427 9.50e-02 1.11e+02   1.92e-01 2.25e+01
        pdb=" NE  ARG B 304 "    0.026 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 304 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 304 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 304 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L   8 "   -0.408 9.50e-02 1.11e+02   1.83e-01 2.05e+01
        pdb=" NE  ARG L   8 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG L   8 "    0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG L   8 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG L   8 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG L   9 "    0.269 9.50e-02 1.11e+02   1.21e-01 9.03e+00
        pdb=" NE  ARG L   9 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  ARG L   9 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG L   9 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG L   9 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1159 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 97
        2.67 -     3.23: 6177
        3.23 -     3.79: 10536
        3.79 -     4.34: 14301
        4.34 -     4.90: 24038
  Nonbonded interactions: 55149
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  47 "
            pdb="MG    MG A 401 "
     model   vdw
     2.113 2.170
  nonbonded pdb=" O   HIS B 142 "
            pdb=" OG1 THR B 143 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OD1 ASP B 247 "
            pdb=" OG1 THR B 249 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OG  SER B  67 "
            pdb=" OD1 ASP B 322 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" NE  ARG B 283 "
            pdb=" OD1 ASP B 298 "
     model   vdw
     2.321 3.120
  ... (remaining 55144 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:             2.150
  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:             0.020
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.930
  Find NCS groups from input model:        0.020
  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:6.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7047
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   0.035   6828  Z= 0.210
  Angle     :  0.606   7.348   9325  Z= 0.369
  Chirality :  0.044   0.207   1115
  Planarity :  0.009   0.192   1162
  Dihedral  : 15.540 167.292   2229
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.36 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 16.61 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.62 (0.28), residues: 891
  helix:  2.72 (0.25), residues: 397
  sheet:  1.30 (0.41), residues: 160
  loop : -1.19 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L   9 
 TYR   0.011   0.001   TYR L  11 
 PHE   0.012   0.001   PHE R 247 
 TRP   0.011   0.001   TRP B  63 
 HIS   0.004   0.001   HIS B 266 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6827)
  covalent geometry    : angle       0.60579 ( 9323)
  SS BOND              : bond        0.00209 (    1)
  SS BOND              : angle       0.41718 (    2)
  hydrogen bonds       : bond        0.14230 (  401)
  hydrogen bonds       : angle       5.30237 ( 1152)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.254 
Fit side-chains
  outliers start: 4
  outliers final: 3
  residues processed: 99
  average time/residue: 0.5194
  time to fit residues: 54.4324
Evaluate side-chains
  96 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain R residue  267 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  18 GLN
R 240 ASN
R 350 ASN
A 269 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.199979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.164340 restraints weight = 7101.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3926 rms_B_bonded: 1.73
r_work: 0.3764 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3669 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.0949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6828  Z= 0.166
  Angle     :  0.572   8.627   9325  Z= 0.301
  Chirality :  0.043   0.139   1115
  Planarity :  0.004   0.045   1162
  Dihedral  :  9.469 168.074    987
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 14.40 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.28), residues: 891
  helix:  2.90 (0.25), residues: 394
  sheet:  1.00 (0.39), residues: 168
  loop : -1.22 (0.32), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 251 
 TYR   0.011   0.001   TYR R 339 
 PHE   0.015   0.002   PHE R 345 
 TRP   0.012   0.002   TRP B  63 
 HIS   0.004   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6827)
  covalent geometry    : angle       0.57178 ( 9323)
  SS BOND              : bond        0.00415 (    1)
  SS BOND              : angle       0.56019 (    2)
  hydrogen bonds       : bond        0.05264 (  401)
  hydrogen bonds       : angle       4.55453 ( 1152)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.247 
Fit side-chains
REVERT: B  322 ASP cc_start: 0.7194 (OUTLIER) cc_final: 0.6984 (p0)
REVERT: R  240 ASN cc_start: 0.8031 (t0) cc_final: 0.7824 (t0)
  outliers start: 25
  outliers final: 11
  residues processed: 107
  average time/residue: 0.4887
  time to fit residues: 55.3486
Evaluate side-chains
  107 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain R residue  124 LEU
Chi-restraints excluded: chain R residue  148 ARG
Chi-restraints excluded: chain R residue  149 ASP
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  260 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   chunk 35 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 350 ASN
A 269 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.197626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.161908 restraints weight = 6987.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 1.74
r_work: 0.3730 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3639 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
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   0.044   6828  Z= 0.212
  Angle     :  0.625   9.541   9325  Z= 0.328
  Chirality :  0.045   0.147   1115
  Planarity :  0.005   0.045   1162
  Dihedral  :  9.707 169.522    985
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 14.72 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.45 (0.28), residues: 891
  helix:  2.71 (0.25), residues: 393
  sheet:  0.94 (0.39), residues: 167
  loop : -1.30 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 137 
 TYR   0.011   0.002   TYR R 319 
 PHE   0.018   0.002   PHE B 151 
 TRP   0.016   0.002   TRP B  63 
 HIS   0.004   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 6827)
  covalent geometry    : angle       0.62538 ( 9323)
  SS BOND              : bond        0.00523 (    1)
  SS BOND              : angle       0.84535 (    2)
  hydrogen bonds       : bond        0.05913 (  401)
  hydrogen bonds       : angle       4.63354 ( 1152)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 95
  time to evaluate  : 0.228 
Fit side-chains
REVERT: B   45 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7043 (mtt)
REVERT: B   79 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7948 (pp)
REVERT: B  318 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8147 (pt)
REVERT: B  322 ASP cc_start: 0.7418 (OUTLIER) cc_final: 0.7147 (p0)
REVERT: C   52 THR cc_start: 0.5331 (OUTLIER) cc_final: 0.5071 (p)
REVERT: R  240 ASN cc_start: 0.8066 (t0) cc_final: 0.7841 (t0)
REVERT: A  309 ASP cc_start: 0.7402 (p0) cc_final: 0.7079 (m-30)
  outliers start: 34
  outliers final: 17
  residues processed: 113
  average time/residue: 0.4766
  time to fit residues: 57.2683
Evaluate side-chains
  116 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain B residue  304 ARG
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  322 ASP
Chi-restraints excluded: chain C residue   52 THR
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  124 LEU
Chi-restraints excluded: chain R residue  148 ARG
Chi-restraints excluded: chain R residue  149 ASP
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  324 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 340 ASN
R 350 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.200188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.164484 restraints weight = 7108.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3902 rms_B_bonded: 1.69
r_work: 0.3747 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3650 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6828  Z= 0.131
  Angle     :  0.528   9.762   9325  Z= 0.276
  Chirality :  0.042   0.142   1115
  Planarity :  0.004   0.044   1162
  Dihedral  :  9.397 167.101    985
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.09 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.66 (0.28), residues: 891
  helix:  2.95 (0.25), residues: 393
  sheet:  0.99 (0.39), residues: 167
  loop : -1.26 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 205 
 TYR   0.011   0.001   TYR R 339 
 PHE   0.013   0.001   PHE A 191 
 TRP   0.012   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6827)
  covalent geometry    : angle       0.52815 ( 9323)
  SS BOND              : bond        0.00360 (    1)
  SS BOND              : angle       0.62291 (    2)
  hydrogen bonds       : bond        0.04674 (  401)
  hydrogen bonds       : angle       4.33514 ( 1152)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.239 
Fit side-chains
REVERT: B   79 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7813 (pp)
REVERT: A  269 ASN cc_start: 0.7321 (t0) cc_final: 0.7119 (m-40)
  outliers start: 22
  outliers final: 9
  residues processed: 107
  average time/residue: 0.4806
  time to fit residues: 54.6712
Evaluate side-chains
  106 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  260 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 74 optimal weight:    0.5980
   chunk 2 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0980
   chunk 21 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
R 240 ASN
R 350 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.202187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.166800 restraints weight = 7153.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3949 rms_B_bonded: 1.77
r_work: 0.3788 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3696 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.1338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6828  Z= 0.112
  Angle     :  0.499   9.887   9325  Z= 0.259
  Chirality :  0.041   0.139   1115
  Planarity :  0.003   0.042   1162
  Dihedral  :  9.138 164.313    985
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.30 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 (0.29), residues: 891
  helix:  3.10 (0.25), residues: 396
  sheet:  0.91 (0.38), residues: 172
  loop : -1.15 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 205 
 TYR   0.011   0.001   TYR R 339 
 PHE   0.011   0.001   PHE B 151 
 TRP   0.012   0.001   TRP B 339 
 HIS   0.002   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 6827)
  covalent geometry    : angle       0.49929 ( 9323)
  SS BOND              : bond        0.00283 (    1)
  SS BOND              : angle       0.46251 (    2)
  hydrogen bonds       : bond        0.04147 (  401)
  hydrogen bonds       : angle       4.14074 ( 1152)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.262 
Fit side-chains
REVERT: B   45 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6928 (mtt)
REVERT: B   79 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7700 (pp)
REVERT: B  142 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7664 (m-70)
  outliers start: 24
  outliers final: 13
  residues processed: 111
  average time/residue: 0.4894
  time to fit residues: 57.5573
Evaluate side-chains
  110 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  124 LEU
Chi-restraints excluded: chain R residue  149 ASP
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  260 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 78 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
R 240 ASN
R 350 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.200868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.165254 restraints weight = 7196.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.3937 rms_B_bonded: 1.70
r_work: 0.3781 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3691 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6828  Z= 0.123
  Angle     :  0.515  10.238   9325  Z= 0.267
  Chirality :  0.042   0.139   1115
  Planarity :  0.003   0.042   1162
  Dihedral  :  9.126 165.752    985
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.77 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 (0.29), residues: 891
  helix:  3.11 (0.25), residues: 396
  sheet:  0.90 (0.38), residues: 172
  loop : -1.15 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 205 
 TYR   0.011   0.001   TYR R 339 
 PHE   0.013   0.001   PHE A 191 
 TRP   0.011   0.001   TRP B 339 
 HIS   0.003   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6827)
  covalent geometry    : angle       0.51539 ( 9323)
  SS BOND              : bond        0.00327 (    1)
  SS BOND              : angle       0.49274 (    2)
  hydrogen bonds       : bond        0.04405 (  401)
  hydrogen bonds       : angle       4.18637 ( 1152)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.253 
Fit side-chains
REVERT: B   45 MET cc_start: 0.7553 (OUTLIER) cc_final: 0.6917 (mtt)
REVERT: B   79 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7799 (pp)
REVERT: R  184 ARG cc_start: 0.7400 (ttp80) cc_final: 0.7166 (ttp-110)
  outliers start: 24
  outliers final: 14
  residues processed: 106
  average time/residue: 0.5234
  time to fit residues: 58.6794
Evaluate side-chains
  109 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  124 LEU
Chi-restraints excluded: chain R residue  148 ARG
Chi-restraints excluded: chain R residue  149 ASP
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  260 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 38 optimal weight:    8.9990
   chunk 78 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 67 optimal weight:    0.1980
   chunk 22 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 9 optimal weight:    0.4980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
R 240 ASN
R 350 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.202684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.167286 restraints weight = 7078.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 1.74
r_work: 0.3804 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3711 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6828  Z= 0.105
  Angle     :  0.489  10.172   9325  Z= 0.253
  Chirality :  0.041   0.136   1115
  Planarity :  0.003   0.042   1162
  Dihedral  :  8.939 167.250    985
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 17.41 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.29), residues: 891
  helix:  3.21 (0.25), residues: 396
  sheet:  0.89 (0.38), residues: 174
  loop : -1.08 (0.34), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 205 
 TYR   0.011   0.001   TYR R 339 
 PHE   0.012   0.001   PHE A 191 
 TRP   0.010   0.001   TRP B 339 
 HIS   0.002   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 6827)
  covalent geometry    : angle       0.48913 ( 9323)
  SS BOND              : bond        0.00257 (    1)
  SS BOND              : angle       0.43882 (    2)
  hydrogen bonds       : bond        0.03947 (  401)
  hydrogen bonds       : angle       4.06013 ( 1152)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 0.269 
Fit side-chains
REVERT: B   45 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6907 (mtt)
REVERT: B   79 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7669 (pp)
REVERT: B  142 HIS cc_start: 0.8194 (OUTLIER) cc_final: 0.7635 (m-70)
REVERT: R  240 ASN cc_start: 0.8121 (t0) cc_final: 0.7919 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 107
  average time/residue: 0.4769
  time to fit residues: 54.2543
Evaluate side-chains
  109 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  124 LEU
Chi-restraints excluded: chain R residue  149 ASP
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  190 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 6 optimal weight:    0.1980
   chunk 84 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
R 350 ASN
A 333 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.199537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.163893 restraints weight = 7044.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3923 rms_B_bonded: 1.68
r_work: 0.3767 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3676 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6828  Z= 0.148
  Angle     :  0.543   9.805   9325  Z= 0.282
  Chirality :  0.043   0.143   1115
  Planarity :  0.004   0.042   1162
  Dihedral  :  9.116 170.477    985
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.56 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 (0.29), residues: 891
  helix:  3.03 (0.25), residues: 396
  sheet:  0.70 (0.37), residues: 181
  loop : -1.13 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 205 
 TYR   0.011   0.001   TYR R 319 
 PHE   0.016   0.001   PHE R 247 
 TRP   0.012   0.002   TRP B  82 
 HIS   0.003   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6827)
  covalent geometry    : angle       0.54259 ( 9323)
  SS BOND              : bond        0.00359 (    1)
  SS BOND              : angle       0.53607 (    2)
  hydrogen bonds       : bond        0.04787 (  401)
  hydrogen bonds       : angle       4.26096 ( 1152)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.236 
Fit side-chains
REVERT: B   45 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.6993 (mtt)
REVERT: B   79 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7885 (pp)
  outliers start: 22
  outliers final: 12
  residues processed: 109
  average time/residue: 0.5013
  time to fit residues: 57.9582
Evaluate side-chains
  110 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  124 LEU
Chi-restraints excluded: chain R residue  149 ASP
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  260 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0570
   chunk 82 optimal weight:    0.4980
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
R 240 ASN
R 350 ASN
A 333 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.201899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.166374 restraints weight = 7132.455|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 1.74
r_work: 0.3792 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3702 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6828  Z= 0.109
  Angle     :  0.494   9.609   9325  Z= 0.257
  Chirality :  0.041   0.136   1115
  Planarity :  0.003   0.042   1162
  Dihedral  :  8.946 170.286    985
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 18.04 %
    Favored  : 78.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.84 (0.29), residues: 891
  helix:  3.13 (0.25), residues: 396
  sheet:  0.73 (0.38), residues: 180
  loop : -1.08 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 205 
 TYR   0.011   0.001   TYR R 339 
 PHE   0.015   0.001   PHE R 247 
 TRP   0.011   0.001   TRP B  82 
 HIS   0.002   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 6827)
  covalent geometry    : angle       0.49358 ( 9323)
  SS BOND              : bond        0.00281 (    1)
  SS BOND              : angle       0.52196 (    2)
  hydrogen bonds       : bond        0.04112 (  401)
  hydrogen bonds       : angle       4.10023 ( 1152)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.254 
Fit side-chains
REVERT: B   45 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.6938 (mtt)
REVERT: B   79 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7691 (pp)
REVERT: B  142 HIS cc_start: 0.8200 (OUTLIER) cc_final: 0.7659 (m-70)
  outliers start: 20
  outliers final: 13
  residues processed: 107
  average time/residue: 0.4880
  time to fit residues: 55.2865
Evaluate side-chains
  111 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  124 LEU
Chi-restraints excluded: chain R residue  149 ASP
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain R residue  308 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  260 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 88 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
R 240 ASN
R 350 ASN
A 333 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.201530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.165890 restraints weight = 7105.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 1.73
r_work: 0.3794 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3703 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6828  Z= 0.116
  Angle     :  0.508   9.659   9325  Z= 0.265
  Chirality :  0.041   0.136   1115
  Planarity :  0.003   0.042   1162
  Dihedral  :  8.933 170.419    985
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.88 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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:  1.85 (0.29), residues: 891
  helix:  3.11 (0.25), residues: 396
  sheet:  0.69 (0.37), residues: 182
  loop : -1.02 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 205 
 TYR   0.011   0.001   TYR R 339 
 PHE   0.016   0.001   PHE A 191 
 TRP   0.011   0.001   TRP B 339 
 HIS   0.002   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 6827)
  covalent geometry    : angle       0.50792 ( 9323)
  SS BOND              : bond        0.00288 (    1)
  SS BOND              : angle       0.50810 (    2)
  hydrogen bonds       : bond        0.04197 (  401)
  hydrogen bonds       : angle       4.10289 ( 1152)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.259 
Fit side-chains
REVERT: B   45 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.6950 (mtt)
REVERT: B   79 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7723 (pp)
REVERT: B  142 HIS cc_start: 0.8206 (OUTLIER) cc_final: 0.7658 (m-70)
REVERT: R  240 ASN cc_start: 0.8165 (t0) cc_final: 0.7956 (t0)
REVERT: A  309 ASP cc_start: 0.7360 (p0) cc_final: 0.7097 (m-30)
  outliers start: 18
  outliers final: 12
  residues processed: 106
  average time/residue: 0.5213
  time to fit residues: 58.4677
Evaluate side-chains
  109 residues out of total 779 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue   45 MET
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain R residue  120 MET
Chi-restraints excluded: chain R residue  124 LEU
Chi-restraints excluded: chain R residue  149 ASP
Chi-restraints excluded: chain R residue  201 VAL
Chi-restraints excluded: chain R residue  232 THR
Chi-restraints excluded: chain R residue  267 VAL
Chi-restraints excluded: chain A residue  190 THR
Chi-restraints excluded: chain A residue  260 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
R 350 ASN
A 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.201139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.165421 restraints weight = 7084.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 1.73
r_work: 0.3791 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3701 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6828  Z= 0.122
  Angle     :  0.513   9.634   9325  Z= 0.268
  Chirality :  0.042   0.137   1115
  Planarity :  0.003   0.042   1162
  Dihedral  :  8.938 169.977    985
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.51 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    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 (0.29), residues: 891
  helix:  3.09 (0.25), residues: 396
  sheet:  0.71 (0.37), residues: 180
  loop : -1.05 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 205 
 TYR   0.011   0.001   TYR R 339 
 PHE   0.017   0.001   PHE A 191 
 TRP   0.011   0.001   TRP B 339 
 HIS   0.002   0.001   HIS R 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 6827)
  covalent geometry    : angle       0.51279 ( 9323)
  SS BOND              : bond        0.00303 (    1)
  SS BOND              : angle       0.52494 (    2)
  hydrogen bonds       : bond        0.04327 (  401)
  hydrogen bonds       : angle       4.13217 ( 1152)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3008.50 seconds
wall clock time: 51 minutes 52.39 seconds (3112.39 seconds total)