Starting phenix.real_space_refine
on Wed Sep 17 10:21:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dtg_47155/09_2025/9dtg_47155.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dtg_47155/09_2025/9dtg_47155.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dtg_47155/09_2025/9dtg_47155.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dtg_47155/09_2025/9dtg_47155.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dtg_47155/09_2025/9dtg_47155.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dtg_47155/09_2025/9dtg_47155.map"
  }
  resolution = 3.83
  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=   0.023
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: 4
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    5104      2.51       5
     N    1386      2.21       5
     O    1533      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8069
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 4039
          Classifications: {'peptide': 512}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 496}
    Chain: "B"
      Number of atoms: 4030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 511, 4030
          Classifications: {'peptide': 511}
          Link IDs: {'PTRANS': 15, 'TRANS': 495}
          Chain breaks: 1
  Time building chain proxies: 2.01, per 1000 atoms: 0.25
  Number of scatterers: 8069
  At special positions: 0
  Unit cell: (74.34, 98.235, 138.945, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    1533      8.00
     N    1386      7.00
     C    5104      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 147 " - pdb=" SG  CYS A 169 " 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: 0.61
  Conformation dependent library (CDL) restraints added in 400.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1934

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 19 sheets defined
      24.5% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 67
      removed outlier: 3.723A  pdb=" N   GLN A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 76
    Processing helix  chain 'A' and resid 78 through 83
      removed outlier: 4.077A  pdb=" N   HIS A  82 " --> pdb=" O   LYS A  79 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ASN A  83 " --> pdb=" O   GLU A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 105
      removed outlier: 4.074A  pdb=" N   GLN A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   LEU A  98 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   TYR A 104 " --> pdb=" O   VAL A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 115
      removed outlier: 3.555A  pdb=" N   LEU A 115 " --> pdb=" O   ALA A 112 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 112 through 115'
    Processing helix  chain 'A' and resid 116 through 125
      removed outlier: 3.643A  pdb=" N   GLU A 120 " --> pdb=" O   GLN A 116 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL A 121 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   SER A 122 " --> pdb=" O   ILE A 118 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASP A 123 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   MET A 124 " --> pdb=" O   GLU A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 139
      removed outlier: 4.204A  pdb=" N   ARG A 136 " --> pdb=" O   GLU A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 155
    Processing helix  chain 'A' and resid 159 through 164
      removed outlier: 3.554A  pdb=" N   THR A 164 " --> pdb=" O   PRO A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 178
      removed outlier: 3.640A  pdb=" N   LEU A 177 " --> pdb=" O   HIS A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 185
      removed outlier: 3.934A  pdb=" N   LEU A 184 " --> pdb=" O   THR A 180 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   HIS A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 180 through 185'
    Processing helix  chain 'A' and resid 187 through 195
      removed outlier: 4.205A  pdb=" N   ASP A 193 " --> pdb=" O   ARG A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 198
      No H-bonds generated for 'chain 'A' and resid 196 through 198'
    Processing helix  chain 'A' and resid 204 through 213
      removed outlier: 3.718A  pdb=" N   ILE A 209 " --> pdb=" O   PRO A 205 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   GLU A 210 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 230
      removed outlier: 4.233A  pdb=" N   GLU A 225 " --> pdb=" O   GLU A 221 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   SER A 226 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   THR A 229 " --> pdb=" O   GLU A 225 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   SER A 230 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 461
      removed outlier: 3.927A  pdb=" N   TRP A 460 " --> pdb=" O   PRO A 457 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER A 461 " --> pdb=" O   GLU A 458 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 457 through 461'
    Processing helix  chain 'B' and resid 31 through 39
      removed outlier: 3.688A  pdb=" N   LYS B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   LEU B  37 " --> pdb=" O   GLY B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 67
      removed outlier: 3.572A  pdb=" N   LEU B  63 " --> pdb=" O   HIS B  59 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   SER B  64 " --> pdb=" O   ARG B  60 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ALA B  65 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLN B  66 " --> pdb=" O   VAL B  62 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 75
      removed outlier: 3.652A  pdb=" N   PHE B  74 " --> pdb=" O   PHE B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 104
      removed outlier: 3.538A  pdb=" N   GLN B  97 " --> pdb=" O   GLU B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 125
    Processing helix  chain 'B' and resid 129 through 132
    Processing helix  chain 'B' and resid 133 through 139
      removed outlier: 3.656A  pdb=" N   LEU B 138 " --> pdb=" O   CYS B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 147
    Processing helix  chain 'B' and resid 148 through 155
    Processing helix  chain 'B' and resid 159 through 164
    Processing helix  chain 'B' and resid 167 through 172
      removed outlier: 4.159A  pdb=" N   THR B 172 " --> pdb=" O   HIS B 168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 180
      removed outlier: 4.329A  pdb=" N   ASN B 179 " --> pdb=" O   ALA B 175 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   THR B 180 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 180 through 185
      removed outlier: 3.965A  pdb=" N   LEU B 184 " --> pdb=" O   THR B 180 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   HIS B 185 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 180 through 185'
    Processing helix  chain 'B' and resid 187 through 196
      removed outlier: 3.522A  pdb=" N   THR B 192 " --> pdb=" O   HIS B 188 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ASP B 193 " --> pdb=" O   ARG B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 214
      removed outlier: 3.746A  pdb=" N   ALA B 208 " --> pdb=" O   ASN B 204 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ILE B 209 " --> pdb=" O   PRO B 205 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   TRP B 212 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 219 through 223
      removed outlier: 3.880A  pdb=" N   ALA B 222 " --> pdb=" O   GLU B 219 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   PHE B 223 " --> pdb=" O   ARG B 220 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 219 through 223'
    Processing helix  chain 'B' and resid 326 through 330
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51
    Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 200
      removed outlier: 6.291A  pdb=" N   VAL A 199 " --> pdb=" O   ILE A 234 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 271
      removed outlier: 5.241A  pdb=" N   SER A 256 " --> pdb=" O   SER A 268 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   GLN A 270 " --> pdb=" O   ALA A 254 " (cutoff:3.500A)
      removed outlier: 5.646A  pdb=" N   ALA A 254 " --> pdb=" O   GLN A 270 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE A 243 " --> pdb=" O   VAL A 516 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 279
      removed outlier: 6.892A  pdb=" N   VAL A 290 " --> pdb=" O   THR A 278 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASP A 286 " --> pdb=" O   HIS A 283 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 277 through 279
      removed outlier: 6.892A  pdb=" N   VAL A 290 " --> pdb=" O   THR A 278 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY A 291 " --> pdb=" O   ARG A 297 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 326
      removed outlier: 3.555A  pdb=" N   VAL A 324 " --> pdb=" O   TYR A 333 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   VAL A 326 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ALA A 331 " --> pdb=" O   VAL A 326 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   TYR A 351 " --> pdb=" O   ILE A 332 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 372 through 374
    Processing sheet with id=AA9, first strand: chain 'A' and resid 386 through 388
    Processing sheet with id=AB1, first strand: chain 'A' and resid 424 through 428
    Processing sheet with id=AB2, first strand: chain 'A' and resid 469 through 472
      removed outlier: 3.744A  pdb=" N   CYS A 472 " --> pdb=" O   SER A 475 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 47 through 49
      removed outlier: 3.536A  pdb=" N   VAL B  47 " --> pdb=" O   LEU B  58 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 199 through 200
      removed outlier: 5.666A  pdb=" N   VAL B 199 " --> pdb=" O   ILE B 234 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 270 through 272
      removed outlier: 4.098A  pdb=" N   ASN B 271 " --> pdb=" O   ALA B 254 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU B 257 " --> pdb=" O   ILE B 240 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE B 515 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 277 through 283
      removed outlier: 3.579A  pdb=" N   GLY B 291 " --> pdb=" O   ARG B 297 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ARG B 297 " --> pdb=" O   GLY B 291 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 322 through 323
    Processing sheet with id=AB8, first strand: chain 'B' and resid 372 through 376
      removed outlier: 3.887A  pdb=" N   CYS B 402 " --> pdb=" O   HIS B 411 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   HIS B 411 " --> pdb=" O   CYS B 402 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 424 through 428
      removed outlier: 3.607A  pdb=" N   ALA B 426 " --> pdb=" O   PHE B 433 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE B 433 " --> pdb=" O   ALA B 426 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   VAL B 432 " --> pdb=" O   TYR B 444 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 467 through 472
      removed outlier: 3.643A  pdb=" N   CYS B 472 " --> pdb=" O   SER B 475 " (cutoff:3.500A)

    164 hydrogen bonds defined for protein.
    414 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: 0.90

  Time building geometry restraints manager: 0.84 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: 2441
        1.33 -     1.45: 1225
        1.45 -     1.57: 4517
        1.57 -     1.69: 1
        1.69 -     1.81: 60
  Bond restraints: 8244
  Sorted by residual:
  bond pdb=" N   SER A 325 "
       pdb=" CA  SER A 325 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.26e-02 6.30e+03 1.06e+01
  bond pdb=" N   VAL A 326 "
       pdb=" CA  VAL A 326 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.039 1.23e-02 6.61e+03 9.96e+00
  bond pdb=" N   LYS A 329 "
       pdb=" CA  LYS A 329 "
    ideal  model  delta    sigma   weight residual
    1.462  1.499 -0.037 1.32e-02 5.74e+03 7.76e+00
  bond pdb=" N   LYS B 329 "
       pdb=" CA  LYS B 329 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.19e-02 7.06e+03 6.80e+00
  bond pdb=" CA  SER A 325 "
       pdb=" CB  SER A 325 "
    ideal  model  delta    sigma   weight residual
    1.534  1.489  0.044 1.72e-02 3.38e+03 6.66e+00
  ... (remaining 8239 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.17: 11013
        2.17 -     4.33: 151
        4.33 -     6.50: 20
        6.50 -     8.66: 5
        8.66 -    10.83: 3
  Bond angle restraints: 11192
  Sorted by residual:
  angle pdb=" N   ASP B  12 "
        pdb=" CA  ASP B  12 "
        pdb=" C   ASP B  12 "
      ideal   model   delta    sigma   weight residual
     112.54  104.48    8.06 1.51e+00 4.39e-01 2.85e+01
  angle pdb=" N   GLY A 328 "
        pdb=" CA  GLY A 328 "
        pdb=" C   GLY A 328 "
      ideal   model   delta    sigma   weight residual
     115.73  107.56    8.17 1.59e+00 3.96e-01 2.64e+01
  angle pdb=" C   LYS A 429 "
        pdb=" CA  LYS A 429 "
        pdb=" CB  LYS A 429 "
      ideal   model   delta    sigma   weight residual
     116.54  110.68    5.86 1.15e+00 7.56e-01 2.59e+01
  angle pdb=" N   MET A  11 "
        pdb=" CA  MET A  11 "
        pdb=" C   MET A  11 "
      ideal   model   delta    sigma   weight residual
     113.23  107.71    5.52 1.24e+00 6.50e-01 1.98e+01
  angle pdb=" C   ALA A   9 "
        pdb=" N   SER A  10 "
        pdb=" CA  SER A  10 "
      ideal   model   delta    sigma   weight residual
     121.54  129.74   -8.20 1.91e+00 2.74e-01 1.84e+01
  ... (remaining 11187 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4391
       17.97 -    35.94: 414
       35.94 -    53.91: 90
       53.91 -    71.88: 12
       71.88 -    89.86: 2
  Dihedral angle restraints: 4909
    sinusoidal: 1919
      harmonic: 2990
  Sorted by residual:
  dihedral pdb=" CA  TYR B 104 "
           pdb=" C   TYR B 104 "
           pdb=" N   HIS B 105 "
           pdb=" CA  HIS B 105 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.64  -26.36     0      5.00e+00 4.00e-02 2.78e+01
  dihedral pdb=" CA  MET B  11 "
           pdb=" C   MET B  11 "
           pdb=" N   ASP B  12 "
           pdb=" CA  ASP B  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.36   21.64     0      5.00e+00 4.00e-02 1.87e+01
  dihedral pdb=" CA  VAL B  17 "
           pdb=" C   VAL B  17 "
           pdb=" N   ASN B  18 "
           pdb=" CA  ASN B  18 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.89   18.11     0      5.00e+00 4.00e-02 1.31e+01
  ... (remaining 4906 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1117
       0.063 -    0.126: 136
       0.126 -    0.188: 12
       0.188 -    0.251: 1
       0.251 -    0.314: 1
  Chirality restraints: 1267
  Sorted by residual:
  chirality pdb=" CB  VAL A 326 "
            pdb=" CA  VAL A 326 "
            pdb=" CG1 VAL A 326 "
            pdb=" CG2 VAL A 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.46e+00
  chirality pdb=" CA  VAL B 326 "
            pdb=" N   VAL B 326 "
            pdb=" C   VAL B 326 "
            pdb=" CB  VAL B 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  VAL A 326 "
            pdb=" N   VAL A 326 "
            pdb=" C   VAL A 326 "
            pdb=" CB  VAL A 326 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.40e-01
  ... (remaining 1264 not shown)

  Planarity restraints: 1438
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 294 "   -0.033 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO B 295 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 295 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 295 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  20 "   -0.007 2.00e-02 2.50e+03   1.38e-02 1.91e+00
        pdb=" C   THR B  20 "    0.024 2.00e-02 2.50e+03
        pdb=" O   THR B  20 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   PHE B  21 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 500 "   -0.006 2.00e-02 2.50e+03   1.25e-02 1.57e+00
        pdb=" C   VAL A 500 "    0.022 2.00e-02 2.50e+03
        pdb=" O   VAL A 500 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   THR A 501 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1435 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 565
        2.74 -     3.28: 7605
        3.28 -     3.82: 11608
        3.82 -     4.36: 13755
        4.36 -     4.90: 23817
  Nonbonded interactions: 57350
  Sorted by model distance:
  nonbonded pdb=" O   SER B 196 "
            pdb=" OG  SER B 196 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG1 THR A 339 "
            pdb=" OG1 THR A 343 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   THR A 490 "
            pdb=" OG1 THR A 490 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG  SER B 247 "
            pdb=" OG1 THR B 511 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OD1 ASN A 271 "
            pdb=" NE1 TRP A 308 "
     model   vdw
     2.282 3.120
  ... (remaining 57345 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 7 through 216 or resid 218 through 518))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.750
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.300
  Find NCS groups from input model:        0.130
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
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   0.046   8245  Z= 0.166
  Angle     :  0.651  10.829  11194  Z= 0.368
  Chirality :  0.044   0.314   1267
  Planarity :  0.003   0.048   1438
  Dihedral  : 14.386  89.856   2972
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.24 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 22.16 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 aren not related in a simple way.
  whole: -3.94 (0.24), residues: 1017
  helix: -3.59 (0.26), residues: 224
  sheet: -2.59 (0.35), residues: 218
  loop : -2.20 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 111 
 TYR   0.016   0.001   TYR A 241 
 PHE   0.008   0.001   PHE B  16 
 TRP   0.012   0.001   TRP A 310 
 HIS   0.002   0.001   HIS B 105 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8244)
  covalent geometry    : angle       0.65075 (11192)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       0.62975 (    2)
  hydrogen bonds       : bond        0.33424 (  163)
  hydrogen bonds       : angle      11.40189 (  414)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.235 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 83
  average time/residue: 0.1007
  time to fit residues: 11.3758
Evaluate side-chains
  78 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 74
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  243 ILE
Chi-restraints excluded: chain A residue  326 VAL
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue  105 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0970
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
A 375 ASN
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 512 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.175320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.162359 restraints weight = 8560.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.160839 restraints weight = 17933.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.159579 restraints weight = 19827.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.158379 restraints weight = 19634.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.157736 restraints weight = 20716.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.1202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8245  Z= 0.153
  Angle     :  0.565   8.319  11194  Z= 0.298
  Chirality :  0.044   0.148   1267
  Planarity :  0.004   0.029   1438
  Dihedral  :  4.811  42.514   1112
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.93 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 19.57 %
    Favored  : 76.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 aren not related in a simple way.
  whole: -4.03 (0.23), residues: 1017
  helix: -3.20 (0.26), residues: 240
  sheet: -2.66 (0.34), residues: 214
  loop : -2.43 (0.23), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 111 
 TYR   0.018   0.002   TYR B 119 
 PHE   0.013   0.001   PHE B  96 
 TRP   0.009   0.001   TRP B 212 
 HIS   0.003   0.001   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 8244)
  covalent geometry    : angle       0.56516 (11192)
  SS BOND              : bond        0.00048 (    1)
  SS BOND              : angle       0.44103 (    2)
  hydrogen bonds       : bond        0.04314 (  163)
  hydrogen bonds       : angle       6.58560 (  414)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 93
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8460 (tppt) cc_final: 0.7881 (ttmt)
  outliers start: 39
  outliers final: 20
  residues processed: 123
  average time/residue: 0.0889
  time to fit residues: 15.3483
Evaluate side-chains
  99 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  359 THR
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 78 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 75 optimal weight:    7.9990
   chunk 96 optimal weight:    0.1980
   chunk 13 optimal weight:    0.6980
   chunk 2 optimal weight:    0.2980
   chunk 4 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 489 ASN
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.176001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.159544 restraints weight = 8551.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 76)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.155555 restraints weight = 15184.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.154218 restraints weight = 20207.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.153079 restraints weight = 18801.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.151652 restraints weight = 19205.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.1479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8245  Z= 0.115
  Angle     :  0.525   9.575  11194  Z= 0.276
  Chirality :  0.043   0.156   1267
  Planarity :  0.003   0.028   1438
  Dihedral  :  4.617  48.089   1109
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.24 %
    Favored  : 90.66 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 20.02 %
    Favored  : 76.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 aren not related in a simple way.
  whole: -3.94 (0.23), residues: 1017
  helix: -3.00 (0.27), residues: 244
  sheet: -2.60 (0.34), residues: 203
  loop : -2.46 (0.23), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 111 
 TYR   0.015   0.002   TYR B 119 
 PHE   0.010   0.001   PHE B  96 
 TRP   0.008   0.001   TRP A 310 
 HIS   0.002   0.001   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8244)
  covalent geometry    : angle       0.52481 (11192)
  SS BOND              : bond        0.00082 (    1)
  SS BOND              : angle       0.31836 (    2)
  hydrogen bonds       : bond        0.03382 (  163)
  hydrogen bonds       : angle       5.70394 (  414)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 82
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8494 (tppt) cc_final: 0.7916 (ttmt)
  outliers start: 34
  outliers final: 22
  residues processed: 109
  average time/residue: 0.0853
  time to fit residues: 13.1551
Evaluate side-chains
  99 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 77
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   15 TYR
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  447 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 82 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0970
   chunk 0 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 45 optimal weight:    9.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 178 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.172380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.158624 restraints weight = 8799.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.155198 restraints weight = 12949.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.154238 restraints weight = 18262.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.141223 restraints weight = 17232.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.138802 restraints weight = 17548.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8245  Z= 0.163
  Angle     :  0.560   8.820  11194  Z= 0.292
  Chirality :  0.044   0.155   1267
  Planarity :  0.003   0.029   1438
  Dihedral  :  4.882  53.123   1109
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.03 %
    Favored  : 89.87 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 18.90 %
    Favored  : 75.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 aren not related in a simple way.
  whole: -3.88 (0.24), residues: 1017
  helix: -2.95 (0.27), residues: 243
  sheet: -2.55 (0.33), residues: 220
  loop : -2.39 (0.24), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 220 
 TYR   0.017   0.002   TYR B 119 
 PHE   0.013   0.001   PHE B  96 
 TRP   0.016   0.001   TRP A 299 
 HIS   0.003   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8244)
  covalent geometry    : angle       0.56045 (11192)
  SS BOND              : bond        0.00133 (    1)
  SS BOND              : angle       0.33265 (    2)
  hydrogen bonds       : bond        0.03344 (  163)
  hydrogen bonds       : angle       5.53355 (  414)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 83
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8628 (tppt) cc_final: 0.8093 (ttmt)
REVERT: B   19 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6507 (m-80)
REVERT: B  344 LEU cc_start: 0.1572 (OUTLIER) cc_final: 0.0732 (mt)
  outliers start: 46
  outliers final: 26
  residues processed: 121
  average time/residue: 0.0844
  time to fit residues: 14.4200
Evaluate side-chains
  108 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 80
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  298 MET
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   chunk 55 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 72 optimal weight:    0.0050
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.174485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.156482 restraints weight = 8707.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.155859 restraints weight = 17538.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.154273 restraints weight = 16685.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.152161 restraints weight = 17514.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.151307 restraints weight = 19293.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8245  Z= 0.121
  Angle     :  0.515   8.245  11194  Z= 0.272
  Chirality :  0.043   0.165   1267
  Planarity :  0.003   0.028   1438
  Dihedral  :  4.792  58.569   1109
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  9.73 %
    Favored  : 90.17 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 20.13 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 aren not related in a simple way.
  whole: -3.83 (0.23), residues: 1017
  helix: -2.80 (0.28), residues: 240
  sheet: -2.61 (0.34), residues: 210
  loop : -2.39 (0.23), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 111 
 TYR   0.015   0.002   TYR B 119 
 PHE   0.010   0.001   PHE B  96 
 TRP   0.024   0.001   TRP A 299 
 HIS   0.002   0.000   HIS A 258 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 8244)
  covalent geometry    : angle       0.51531 (11192)
  SS BOND              : bond        0.00135 (    1)
  SS BOND              : angle       0.33184 (    2)
  hydrogen bonds       : bond        0.02920 (  163)
  hydrogen bonds       : angle       5.23694 (  414)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 77
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8577 (tppt) cc_final: 0.8072 (ttmt)
REVERT: A  195 ILE cc_start: 0.8825 (mm) cc_final: 0.8618 (mt)
REVERT: B   12 ASP cc_start: 0.5905 (p0) cc_final: 0.4826 (m-30)
REVERT: B   19 TYR cc_start: 0.7297 (OUTLIER) cc_final: 0.6449 (m-80)
REVERT: B  114 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8139 (pp20)
REVERT: B  344 LEU cc_start: 0.1488 (OUTLIER) cc_final: 0.1235 (mt)
  outliers start: 40
  outliers final: 27
  residues processed: 111
  average time/residue: 0.0763
  time to fit residues: 12.4826
Evaluate side-chains
  103 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 73
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  270 GLN
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  359 THR
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0670
   chunk 83 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0570
   chunk 62 optimal weight:    0.8980
   chunk 99 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   overall best weight:    0.4836

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.174706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.161245 restraints weight = 8527.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.158879 restraints weight = 13193.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.157102 restraints weight = 16177.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.154986 restraints weight = 17857.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.153592 restraints weight = 19903.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8245  Z= 0.119
  Angle     :  0.524  10.639  11194  Z= 0.272
  Chirality :  0.043   0.166   1267
  Planarity :  0.003   0.028   1438
  Dihedral  :  4.775  58.416   1109
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.52 %
    Favored  : 89.38 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 19.91 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 aren not related in a simple way.
  whole: -3.72 (0.23), residues: 1017
  helix: -2.70 (0.28), residues: 239
  sheet: -2.61 (0.34), residues: 205
  loop : -2.31 (0.23), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 352 
 TYR   0.015   0.002   TYR B 119 
 PHE   0.011   0.001   PHE B  96 
 TRP   0.018   0.001   TRP A 299 
 HIS   0.002   0.000   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8244)
  covalent geometry    : angle       0.52376 (11192)
  SS BOND              : bond        0.00124 (    1)
  SS BOND              : angle       0.33336 (    2)
  hydrogen bonds       : bond        0.02775 (  163)
  hydrogen bonds       : angle       5.10674 (  414)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 76
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8564 (tppt) cc_final: 0.8160 (ttmt)
REVERT: B   12 ASP cc_start: 0.5682 (p0) cc_final: 0.4762 (m-30)
REVERT: B   19 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6447 (m-80)
REVERT: B  114 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8197 (pp20)
REVERT: B  344 LEU cc_start: 0.1617 (OUTLIER) cc_final: 0.1280 (mt)
  outliers start: 45
  outliers final: 29
  residues processed: 113
  average time/residue: 0.0767
  time to fit residues: 12.6497
Evaluate side-chains
  102 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 70
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  298 MET
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 42 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 52 optimal weight:    0.3980
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.172469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.156738 restraints weight = 8709.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.151586 restraints weight = 15481.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.150910 restraints weight = 21123.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.150129 restraints weight = 19392.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.149670 restraints weight = 18004.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8245  Z= 0.150
  Angle     :  0.558   9.014  11194  Z= 0.289
  Chirality :  0.044   0.183   1267
  Planarity :  0.003   0.029   1438
  Dihedral  :  4.935  56.150   1109
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.31 %
    Favored  : 88.59 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 20.70 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 aren not related in a simple way.
  whole: -3.78 (0.23), residues: 1017
  helix: -2.70 (0.29), residues: 236
  sheet: -2.58 (0.34), residues: 215
  loop : -2.40 (0.23), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 318 
 TYR   0.018   0.002   TYR B  19 
 PHE   0.013   0.001   PHE B  96 
 TRP   0.010   0.001   TRP A 299 
 HIS   0.003   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 8244)
  covalent geometry    : angle       0.55787 (11192)
  SS BOND              : bond        0.00158 (    1)
  SS BOND              : angle       0.28575 (    2)
  hydrogen bonds       : bond        0.02997 (  163)
  hydrogen bonds       : angle       5.17644 (  414)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 79
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A   22 LYS cc_start: 0.8511 (tppt) cc_final: 0.8089 (ttmt)
REVERT: A  258 HIS cc_start: 0.8358 (t-90) cc_final: 0.7928 (t70)
REVERT: B   12 ASP cc_start: 0.5694 (p0) cc_final: 0.4825 (m-30)
REVERT: B   19 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.6607 (m-80)
REVERT: B  344 LEU cc_start: 0.2008 (OUTLIER) cc_final: 0.1490 (mt)
  outliers start: 46
  outliers final: 34
  residues processed: 116
  average time/residue: 0.0746
  time to fit residues: 12.8161
Evaluate side-chains
  112 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 76
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  270 GLN
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  298 MET
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 81 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 77 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.170137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.153170 restraints weight = 8696.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.141044 restraints weight = 18035.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.138671 restraints weight = 18985.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.136108 restraints weight = 18586.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.137340 restraints weight = 14819.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8245  Z= 0.195
  Angle     :  0.605   8.298  11194  Z= 0.317
  Chirality :  0.046   0.201   1267
  Planarity :  0.004   0.032   1438
  Dihedral  :  5.290  54.411   1109
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 12.29 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 21.26 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 aren not related in a simple way.
  whole: -3.93 (0.23), residues: 1017
  helix: -2.89 (0.28), residues: 238
  sheet: -2.72 (0.31), residues: 236
  loop : -2.38 (0.24), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 422 
 TYR   0.023   0.002   TYR B  19 
 PHE   0.015   0.002   PHE B  16 
 TRP   0.022   0.001   TRP A 299 
 HIS   0.004   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 8244)
  covalent geometry    : angle       0.60494 (11192)
  SS BOND              : bond        0.00244 (    1)
  SS BOND              : angle       0.29973 (    2)
  hydrogen bonds       : bond        0.03309 (  163)
  hydrogen bonds       : angle       5.35660 (  414)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 82
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   22 LYS cc_start: 0.8612 (tppt) cc_final: 0.8118 (ttmt)
REVERT: A  258 HIS cc_start: 0.8345 (t-90) cc_final: 0.7998 (t70)
REVERT: B   19 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.6767 (m-80)
REVERT: B  344 LEU cc_start: 0.2348 (OUTLIER) cc_final: 0.1938 (mt)
  outliers start: 47
  outliers final: 33
  residues processed: 116
  average time/residue: 0.0732
  time to fit residues: 12.4450
Evaluate side-chains
  115 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 80
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  251 HIS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   15 TYR
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  290 VAL
Chi-restraints excluded: chain B residue  298 MET
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  503 THR
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 24 optimal weight:    0.2980
   chunk 65 optimal weight:    0.0770
   chunk 54 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0000
   chunk 33 optimal weight:    3.9990
   chunk 41 optimal weight:    0.1980
   chunk 28 optimal weight:    0.9990
   chunk 95 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.2542

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

Flipped N/Q/H residues before XYZ refinement:
** B  59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.175239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.163522 restraints weight = 8599.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 97)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.145962 restraints weight = 16086.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.142603 restraints weight = 14599.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.141093 restraints weight = 16523.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.141716 restraints weight = 13962.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8245  Z= 0.096
  Angle     :  0.537  10.641  11194  Z= 0.278
  Chirality :  0.042   0.191   1267
  Planarity :  0.003   0.028   1438
  Dihedral  :  4.728  50.005   1109
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.23 %
    Favored  : 89.68 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 22.50 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 aren not related in a simple way.
  whole: -3.68 (0.23), residues: 1017
  helix: -2.66 (0.29), residues: 238
  sheet: -2.52 (0.33), residues: 211
  loop : -2.31 (0.23), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 352 
 TYR   0.014   0.001   TYR B 119 
 PHE   0.010   0.001   PHE B  96 
 TRP   0.021   0.001   TRP A 299 
 HIS   0.003   0.000   HIS A 428 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 8244)
  covalent geometry    : angle       0.53703 (11192)
  SS BOND              : bond        0.00119 (    1)
  SS BOND              : angle       0.45322 (    2)
  hydrogen bonds       : bond        0.02585 (  163)
  hydrogen bonds       : angle       4.96972 (  414)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 79
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   22 LYS cc_start: 0.8588 (tppt) cc_final: 0.8136 (ttmt)
REVERT: A  308 TRP cc_start: 0.8387 (m100) cc_final: 0.7931 (m100)
REVERT: B   19 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6403 (m-80)
REVERT: B   26 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7041 (m170)
REVERT: B  114 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8152 (pp20)
REVERT: B  344 LEU cc_start: 0.2066 (OUTLIER) cc_final: 0.1812 (mt)
  outliers start: 34
  outliers final: 24
  residues processed: 105
  average time/residue: 0.0730
  time to fit residues: 11.4525
Evaluate side-chains
  104 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  276 GLN
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  441 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    2.9990
   chunk 75 optimal weight:    8.9990
   chunk 91 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.170487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.157268 restraints weight = 8675.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.139784 restraints weight = 20246.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.138124 restraints weight = 19358.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.136745 restraints weight = 13728.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.136993 restraints weight = 11464.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8245  Z= 0.181
  Angle     :  0.611  13.478  11194  Z= 0.312
  Chirality :  0.045   0.196   1267
  Planarity :  0.004   0.032   1438
  Dihedral  :  5.058  51.532   1109
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 11.90 %
    Favored  : 88.00 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 22.83 %
    Favored  : 73.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 aren not related in a simple way.
  whole: -3.83 (0.23), residues: 1017
  helix: -2.74 (0.28), residues: 239
  sheet: -2.73 (0.32), residues: 212
  loop : -2.38 (0.23), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 296 
 TYR   0.021   0.002   TYR B  19 
 PHE   0.014   0.001   PHE B  96 
 TRP   0.024   0.001   TRP A 299 
 HIS   0.003   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 8244)
  covalent geometry    : angle       0.61055 (11192)
  SS BOND              : bond        0.00139 (    1)
  SS BOND              : angle       0.27175 (    2)
  hydrogen bonds       : bond        0.03095 (  163)
  hydrogen bonds       : angle       5.16661 (  414)

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 81
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A   22 LYS cc_start: 0.8650 (tppt) cc_final: 0.8178 (ttmt)
REVERT: B   19 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.6710 (m-80)
REVERT: B  114 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8141 (pp20)
REVERT: B  344 LEU cc_start: 0.2222 (OUTLIER) cc_final: 0.1948 (mt)
REVERT: B  383 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6379 (pp)
  outliers start: 35
  outliers final: 25
  residues processed: 107
  average time/residue: 0.0765
  time to fit residues: 11.7872
Evaluate side-chains
  109 residues out of total 889 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 80
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 VAL
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  201 CYS
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  281 CYS
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  450 SER
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain B residue   18 ASN
Chi-restraints excluded: chain B residue   19 TYR
Chi-restraints excluded: chain B residue   26 HIS
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  105 HIS
Chi-restraints excluded: chain B residue  108 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  147 CYS
Chi-restraints excluded: chain B residue  199 VAL
Chi-restraints excluded: chain B residue  267 VAL
Chi-restraints excluded: chain B residue  298 MET
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  344 LEU
Chi-restraints excluded: chain B residue  348 VAL
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  383 LEU
Chi-restraints excluded: chain B residue  441 LEU
Chi-restraints excluded: chain B residue  513 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 91 optimal weight:    9.9990
   chunk 100 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    0.1980
   chunk 81 optimal weight:    4.9990
   chunk 44 optimal weight:    0.4980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.169490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.154779 restraints weight = 8684.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.136372 restraints weight = 16226.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.134964 restraints weight = 16223.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.134413 restraints weight = 16370.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.134666 restraints weight = 13106.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.3081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8245  Z= 0.193
  Angle     :  0.638  15.530  11194  Z= 0.323
  Chirality :  0.046   0.216   1267
  Planarity :  0.004   0.035   1438
  Dihedral  :  5.246  51.688   1109
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 12.29 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 22.61 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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 aren not related in a simple way.
  whole: -3.89 (0.23), residues: 1017
  helix: -2.83 (0.28), residues: 235
  sheet: -2.78 (0.31), residues: 227
  loop : -2.36 (0.24), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 296 
 TYR   0.022   0.002   TYR B  19 
 PHE   0.013   0.002   PHE B  96 
 TRP   0.025   0.001   TRP A 299 
 HIS   0.003   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 8244)
  covalent geometry    : angle       0.63760 (11192)
  SS BOND              : bond        0.00264 (    1)
  SS BOND              : angle       0.22507 (    2)
  hydrogen bonds       : bond        0.03220 (  163)
  hydrogen bonds       : angle       5.30424 (  414)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1366.13 seconds
wall clock time: 24 minutes 21.29 seconds (1461.29 seconds total)