Starting phenix.real_space_refine
on Sat Aug 23 00:14:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ziu_60130/08_2025/8ziu_60130.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ziu_60130/08_2025/8ziu_60130.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ziu_60130/08_2025/8ziu_60130.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ziu_60130/08_2025/8ziu_60130.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ziu_60130/08_2025/8ziu_60130.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ziu_60130/08_2025/8ziu_60130.cif"
  }
  resolution = 3.54
  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=   0.001
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: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      52      5.16       5
     C    5514      2.51       5
     N    1464      2.21       5
     O    1636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8668
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "J"
      Number of atoms: 2887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 370, 2887
          Classifications: {'peptide': 370}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 350}
    Chain: "C"
      Number of atoms: 5754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 715, 5754
          Classifications: {'peptide': 715}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 24, 'TRANS': 690}
          Chain breaks: 5
    Chain: "J"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.71, per 1000 atoms: 0.20
  Number of scatterers: 8668
  At special positions: 0
  Unit cell: (129.48, 92.13, 112.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     P       2     15.00
     O    1636      8.00
     N    1464      7.00
     C    5514      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 224.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2030

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 13 sheets defined
      51.0% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'J' and resid 58 through 63
    Processing helix  chain 'J' and resid 80 through 94
    Processing helix  chain 'J' and resid 99 through 103
    Processing helix  chain 'J' and resid 114 through 129
      removed outlier: 4.135A  pdb=" N   ARG J 118 " --> pdb=" O   PRO J 114 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 139 through 148
    Processing helix  chain 'J' and resid 174 through 177
    Processing helix  chain 'J' and resid 183 through 196
      removed outlier: 3.964A  pdb=" N   THR J 196 " --> pdb=" O   MET J 192 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 197 through 199
      No H-bonds generated for 'chain 'J' and resid 197 through 199'
    Processing helix  chain 'J' and resid 204 through 219
    Processing helix  chain 'J' and resid 224 through 235
    Processing helix  chain 'J' and resid 254 through 259
    Processing helix  chain 'J' and resid 260 through 264
    Processing helix  chain 'J' and resid 265 through 270
      removed outlier: 3.620A  pdb=" N   ILE J 269 " --> pdb=" O   PRO J 266 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLY J 270 " --> pdb=" O   SER J 267 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 275 through 286
    Processing helix  chain 'J' and resid 291 through 297
      removed outlier: 3.951A  pdb=" N   ALA J 297 " --> pdb=" O   LYS J 293 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 304 through 308
      removed outlier: 4.335A  pdb=" N   TYR J 308 " --> pdb=" O   THR J 305 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 310 through 323
      removed outlier: 3.505A  pdb=" N   ARG J 314 " --> pdb=" O   GLY J 310 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 336 through 338
      No H-bonds generated for 'chain 'J' and resid 336 through 338'
    Processing helix  chain 'J' and resid 339 through 351
    Processing helix  chain 'J' and resid 352 through 355
    Processing helix  chain 'J' and resid 361 through 368
    Processing helix  chain 'J' and resid 370 through 375
      removed outlier: 3.781A  pdb=" N   ARG J 374 " --> pdb=" O   SER J 370 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 11
      removed outlier: 3.559A  pdb=" N   PHE C   9 " --> pdb=" O   MET C   6 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLY C  10 " --> pdb=" O   ALA C   7 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   ALA C  11 " --> pdb=" O   ASP C   8 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 6 through 11'
    Processing helix  chain 'C' and resid 12 through 17
    Processing helix  chain 'C' and resid 19 through 27
    Processing helix  chain 'C' and resid 81 through 85
      removed outlier: 3.539A  pdb=" N   ASP C  85 " --> pdb=" O   PRO C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 93
    Processing helix  chain 'C' and resid 97 through 111
    Processing helix  chain 'C' and resid 153 through 169
      removed outlier: 3.694A  pdb=" N   ILE C 157 " --> pdb=" O   HIS C 153 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 199
    Processing helix  chain 'C' and resid 216 through 224
      removed outlier: 3.600A  pdb=" N   ALA C 224 " --> pdb=" O   GLN C 220 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 232
      removed outlier: 3.816A  pdb=" N   LEU C 228 " --> pdb=" O   ALA C 224 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 270 through 274
    Processing helix  chain 'C' and resid 285 through 292
    Processing helix  chain 'C' and resid 295 through 302
      removed outlier: 3.891A  pdb=" N   LEU C 299 " --> pdb=" O   LYS C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 311
      removed outlier: 3.642A  pdb=" N   TYR C 311 " --> pdb=" O   PRO C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 325 through 340
      removed outlier: 3.741A  pdb=" N   GLU C 329 " --> pdb=" O   ASP C 325 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 344 through 361
      removed outlier: 4.097A  pdb=" N   VAL C 350 " --> pdb=" O   GLU C 346 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLY C 361 " --> pdb=" O   ILE C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 379 through 389
    Processing helix  chain 'C' and resid 392 through 402
    Processing helix  chain 'C' and resid 417 through 448
    Processing helix  chain 'C' and resid 473 through 505
    Processing helix  chain 'C' and resid 515 through 520
    Processing helix  chain 'C' and resid 521 through 526
      removed outlier: 3.702A  pdb=" N   LEU C 524 " --> pdb=" O   CYS C 521 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ILE C 525 " --> pdb=" O   ILE C 522 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 530 through 541
    Processing helix  chain 'C' and resid 545 through 558
    Processing helix  chain 'C' and resid 593 through 599
      removed outlier: 3.736A  pdb=" N   LYS C 599 " --> pdb=" O   LEU C 595 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 603 through 611
    Processing helix  chain 'C' and resid 615 through 622
    Processing helix  chain 'C' and resid 648 through 666
      removed outlier: 3.741A  pdb=" N   THR C 666 " --> pdb=" O   THR C 662 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 687 through 698
    Processing helix  chain 'C' and resid 699 through 708
    Processing helix  chain 'C' and resid 716 through 724
      removed outlier: 3.659A  pdb=" N   PHE C 720 " --> pdb=" O   LEU C 716 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 744 through 749
    Processing sheet with id=AA1, first strand: chain 'J' and resid 31 through 33
      removed outlier: 6.844A  pdb=" N   LEU J  10 " --> pdb=" O   LEU J 106 " (cutoff:3.500A)
      removed outlier: 8.237A  pdb=" N   THR J 108 " --> pdb=" O   LEU J  10 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   CYS J  12 " --> pdb=" O   THR J 108 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 55 through 56
    Processing sheet with id=AA3, first strand: chain 'J' and resid 171 through 172
    Processing sheet with id=AA4, first strand: chain 'J' and resid 171 through 172
      removed outlier: 3.587A  pdb=" N   VAL J 154 " --> pdb=" O   VAL J 165 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ASN J 299 " --> pdb=" O   ILE J 332 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'J' and resid 240 through 243
    Processing sheet with id=AA6, first strand: chain 'C' and resid 46 through 49
    Processing sheet with id=AA7, first strand: chain 'C' and resid 63 through 64
      removed outlier: 3.516A  pdb=" N   THR C  63 " --> pdb=" O   VAL C  69 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 115 through 118
      removed outlier: 6.208A  pdb=" N   SER C 173 " --> pdb=" O   HIS C 670 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   VAL C 672 " --> pdb=" O   SER C 173 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   LEU C 175 " --> pdb=" O   VAL C 672 " (cutoff:3.500A)
      removed outlier: 7.610A  pdb=" N   CYS C 674 " --> pdb=" O   LEU C 175 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   THR C 177 " --> pdb=" O   CYS C 674 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   GLN C 172 " --> pdb=" O   GLY C 459 " (cutoff:3.500A)
      removed outlier: 7.545A  pdb=" N   LEU C 461 " --> pdb=" O   GLN C 172 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ILE C 174 " --> pdb=" O   LEU C 461 " (cutoff:3.500A)
      removed outlier: 7.806A  pdb=" N   ILE C 463 " --> pdb=" O   ILE C 174 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   ILE C 176 " --> pdb=" O   ILE C 463 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TYR C 456 " --> pdb=" O   PHE C 253 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   GLY C 246 " --> pdb=" O   THR C 266 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   THR C 266 " --> pdb=" O   GLY C 246 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   PHE C 248 " --> pdb=" O   ILE C 264 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   ILE C 264 " --> pdb=" O   PHE C 248 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   ARG C 250 " --> pdb=" O   ALA C 262 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   ALA C 262 " --> pdb=" O   ARG C 250 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   HIS C 252 " --> pdb=" O   ALA C 260 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 233 through 234
    Processing sheet with id=AB1, first strand: chain 'C' and resid 365 through 367
    Processing sheet with id=AB2, first strand: chain 'C' and resid 404 through 407
    Processing sheet with id=AB3, first strand: chain 'C' and resid 564 through 565
      removed outlier: 3.556A  pdb=" N   PHE C 578 " --> pdb=" O   TYR C 589 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   GLY C 585 " --> pdb=" O   HIS C 582 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 713 through 715

    411 hydrogen bonds defined for protein.
    1131 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.27

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2822
        1.34 -     1.46: 1701
        1.46 -     1.58: 4236
        1.58 -     1.69: 3
        1.69 -     1.81: 90
  Bond restraints: 8852
  Sorted by residual:
  bond pdb=" C4  ADP J 401 "
       pdb=" C5  ADP J 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.465  0.025 2.00e-02 2.50e+03 1.56e+00
  bond pdb=" N   ASN C 135 "
       pdb=" CA  ASN C 135 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.015 1.29e-02 6.01e+03 1.40e+00
  bond pdb=" CB  LEU J 180 "
       pdb=" CG  LEU J 180 "
    ideal  model  delta    sigma   weight residual
    1.530  1.512  0.018 2.00e-02 2.50e+03 7.71e-01
  bond pdb=" C   PRO C 528 "
       pdb=" N   MET C 529 "
    ideal  model  delta    sigma   weight residual
    1.336  1.320  0.015 1.75e-02 3.27e+03 7.49e-01
  bond pdb=" CB  LEU C 291 "
       pdb=" CG  LEU C 291 "
    ideal  model  delta    sigma   weight residual
    1.530  1.514  0.016 2.00e-02 2.50e+03 6.71e-01
  ... (remaining 8847 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 11497
        1.39 -     2.77: 362
        2.77 -     4.16: 71
        4.16 -     5.55: 20
        5.55 -     6.93: 5
  Bond angle restraints: 11955
  Sorted by residual:
  angle pdb=" N   GLY C  66 "
        pdb=" CA  GLY C  66 "
        pdb=" C   GLY C  66 "
      ideal   model   delta    sigma   weight residual
     114.48  109.23    5.25 1.19e+00 7.06e-01 1.94e+01
  angle pdb=" N   ILE C 753 "
        pdb=" CA  ILE C 753 "
        pdb=" C   ILE C 753 "
      ideal   model   delta    sigma   weight residual
     110.23  113.86   -3.63 1.04e+00 9.25e-01 1.22e+01
  angle pdb=" CA  ALA C 136 "
        pdb=" C   ALA C 136 "
        pdb=" N   GLU C 137 "
      ideal   model   delta    sigma   weight residual
     115.75  120.23   -4.48 1.34e+00 5.57e-01 1.12e+01
  angle pdb=" N   ASN C 135 "
        pdb=" CA  ASN C 135 "
        pdb=" CB  ASN C 135 "
      ideal   model   delta    sigma   weight residual
     110.49  105.97    4.52 1.69e+00 3.50e-01 7.16e+00
  angle pdb=" CA  ALA C 136 "
        pdb=" C   ALA C 136 "
        pdb=" O   ALA C 136 "
      ideal   model   delta    sigma   weight residual
     121.46  118.13    3.33 1.25e+00 6.40e-01 7.10e+00
  ... (remaining 11950 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 4863
       17.89 -    35.78: 396
       35.78 -    53.67: 48
       53.67 -    71.56: 15
       71.56 -    89.45: 14
  Dihedral angle restraints: 5336
    sinusoidal: 2179
      harmonic: 3157
  Sorted by residual:
  dihedral pdb=" CA  TYR C 134 "
           pdb=" C   TYR C 134 "
           pdb=" N   ASN C 135 "
           pdb=" CA  ASN C 135 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.81  -28.19     0      5.00e+00 4.00e-02 3.18e+01
  dihedral pdb=" CA  ALA C 111 "
           pdb=" C   ALA C 111 "
           pdb=" N   TRP C 112 "
           pdb=" CA  TRP C 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.88  -25.12     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  PRO C 528 "
           pdb=" C   PRO C 528 "
           pdb=" N   MET C 529 "
           pdb=" CA  MET C 529 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.54   24.46     0      5.00e+00 4.00e-02 2.39e+01
  ... (remaining 5333 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 773
       0.034 -    0.067: 369
       0.067 -    0.101: 111
       0.101 -    0.134: 46
       0.134 -    0.168: 4
  Chirality restraints: 1303
  Sorted by residual:
  chirality pdb=" CG  LEU C 105 "
            pdb=" CB  LEU C 105 "
            pdb=" CD1 LEU C 105 "
            pdb=" CD2 LEU C 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.05e-01
  chirality pdb=" CB  ILE J 153 "
            pdb=" CA  ILE J 153 "
            pdb=" CG1 ILE J 153 "
            pdb=" CG2 ILE J 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.60e-01
  chirality pdb=" CA  ILE C 676 "
            pdb=" N   ILE C 676 "
            pdb=" C   ILE C 676 "
            pdb=" CB  ILE C 676 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.97e-01
  ... (remaining 1300 not shown)

  Planarity restraints: 1540
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C  45 "   -0.007 2.00e-02 2.50e+03   1.51e-02 2.27e+00
        pdb=" C   GLU C  45 "    0.026 2.00e-02 2.50e+03
        pdb=" O   GLU C  45 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR C  46 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 151 "    0.024 5.00e-02 4.00e+02   3.59e-02 2.07e+00
        pdb=" N   PRO C 152 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO C 152 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO C 152 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 225 "   -0.022 5.00e-02 4.00e+02   3.23e-02 1.67e+00
        pdb=" N   PRO C 226 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO C 226 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 226 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1537 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 140
        2.68 -     3.24: 8349
        3.24 -     3.79: 13044
        3.79 -     4.35: 18181
        4.35 -     4.90: 30356
  Nonbonded interactions: 70070
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP J 159 "
            pdb=" O3' ADP J 401 "
     model   vdw
     2.130 3.040
  nonbonded pdb=" OH  TYR C 554 "
            pdb=" O   HIS C 577 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OH  TYR C 115 "
            pdb=" OH  TYR C 134 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" NZ  LYS C  86 "
            pdb=" OE2 GLU C 107 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" O   GLY J 158 "
            pdb=" OG1 THR J 305 "
     model   vdw
     2.228 3.040
  ... (remaining 70065 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             8.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.120
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:0.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8852  Z= 0.183
  Angle     :  0.621   6.934  11955  Z= 0.344
  Chirality :  0.044   0.168   1303
  Planarity :  0.004   0.036   1540
  Dihedral  : 14.017  89.452   3306
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.79 (0.22), residues: 1072
  helix: -1.07 (0.21), residues: 498
  sheet: -1.89 (0.44), residues: 116
  loop : -2.69 (0.23), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J  30 
 TYR   0.016   0.001   TYR C 103 
 PHE   0.012   0.001   PHE C 489 
 TRP   0.012   0.002   TRP J  81 
 HIS   0.005   0.001   HIS C 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 8852)
  covalent geometry    : angle       0.62119 (11955)
  hydrogen bonds       : bond        0.18141 (  409)
  hydrogen bonds       : angle       6.74965 ( 1131)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: C   86 LYS cc_start: 0.7631 (ttmm) cc_final: 0.7397 (mtpp)
REVERT: C  268 LEU cc_start: 0.8706 (pp) cc_final: 0.8275 (pt)
REVERT: C  387 TYR cc_start: 0.8603 (t80) cc_final: 0.8258 (t80)
REVERT: C  516 MET cc_start: 0.6085 (mpp) cc_final: 0.5494 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.0899
  time to fit residues: 11.5521
Evaluate side-chains
  68 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
J  14 ASN
J 103 HIS
J 163 HIS
J 355 GLN
J 356 GLN
C 187 ASN
C 223 GLN
C 285 HIS
C 488 GLN
C 577 HIS
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 713 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.081969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.068659 restraints weight = 18510.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.069186 restraints weight = 10482.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.069751 restraints weight = 8953.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.070295 restraints weight = 7567.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.070395 restraints weight = 7118.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8852  Z= 0.213
  Angle     :  0.619   6.359  11955  Z= 0.319
  Chirality :  0.046   0.190   1303
  Planarity :  0.004   0.035   1540
  Dihedral  :  6.604  88.957   1186
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  6.65 %
    Favored  : 92.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.47 (0.24), residues: 1072
  helix:  0.08 (0.23), residues: 502
  sheet: -1.26 (0.48), residues: 112
  loop : -2.10 (0.25), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 370 
 TYR   0.019   0.002   TYR C 103 
 PHE   0.014   0.002   PHE C 511 
 TRP   0.011   0.002   TRP J 342 
 HIS   0.004   0.001   HIS C 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 8852)
  covalent geometry    : angle       0.61903 (11955)
  hydrogen bonds       : bond        0.04835 (  409)
  hydrogen bonds       : angle       5.04944 ( 1131)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: C   50 LYS cc_start: 0.5844 (mppt) cc_final: 0.5407 (mppt)
REVERT: C  387 TYR cc_start: 0.8402 (t80) cc_final: 0.8176 (t80)
REVERT: C  434 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7120 (tt0)
REVERT: C  516 MET cc_start: 0.6003 (mpp) cc_final: 0.5511 (mpp)
REVERT: C  569 ASN cc_start: 0.7007 (p0) cc_final: 0.6773 (m-40)
  outliers start: 10
  outliers final: 4
  residues processed: 78
  average time/residue: 0.0734
  time to fit residues: 8.0323
Evaluate side-chains
  67 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain C residue  268 LEU
Chi-restraints excluded: chain C residue  434 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
C 487 GLN
** C 678 ASN ** 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 = 0.3189 r_free = 0.3189 target = 0.082158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.068679 restraints weight = 18482.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.070481 restraints weight = 10624.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.070796 restraints weight = 7611.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.071083 restraints weight = 6689.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.071280 restraints weight = 6006.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8852  Z= 0.189
  Angle     :  0.588   8.115  11955  Z= 0.301
  Chirality :  0.044   0.166   1303
  Planarity :  0.004   0.034   1540
  Dihedral  :  6.462  88.228   1186
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  8.26 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.25), residues: 1072
  helix:  0.63 (0.24), residues: 498
  sheet: -0.96 (0.49), residues: 109
  loop : -1.74 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  34 
 TYR   0.019   0.001   TYR C 103 
 PHE   0.011   0.001   PHE J 257 
 TRP   0.012   0.001   TRP J  81 
 HIS   0.003   0.001   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 8852)
  covalent geometry    : angle       0.58751 (11955)
  hydrogen bonds       : bond        0.04383 (  409)
  hydrogen bonds       : angle       4.82605 ( 1131)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
REVERT: C  387 TYR cc_start: 0.8384 (t80) cc_final: 0.8163 (t80)
REVERT: C  434 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7116 (tt0)
REVERT: C  516 MET cc_start: 0.5954 (mpp) cc_final: 0.5433 (mpp)
  outliers start: 11
  outliers final: 8
  residues processed: 71
  average time/residue: 0.0940
  time to fit residues: 9.1199
Evaluate side-chains
  71 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain C residue  268 LEU
Chi-restraints excluded: chain C residue  360 TYR
Chi-restraints excluded: chain C residue  434 GLU
Chi-restraints excluded: chain C residue  440 MET
Chi-restraints excluded: chain C residue  450 THR
Chi-restraints excluded: chain C residue  748 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 16 optimal weight:    0.4980
   chunk 37 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 94 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** C 678 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 = 0.3202 r_free = 0.3202 target = 0.082797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.069190 restraints weight = 18852.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.071162 restraints weight = 10969.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.071442 restraints weight = 7735.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.071771 restraints weight = 6639.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.071914 restraints weight = 6057.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8852  Z= 0.156
  Angle     :  0.553   6.885  11955  Z= 0.282
  Chirality :  0.043   0.159   1303
  Planarity :  0.003   0.033   1540
  Dihedral  :  6.274  86.933   1186
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.12 %
    Favored  : 89.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.26), residues: 1072
  helix:  0.89 (0.25), residues: 501
  sheet: -0.87 (0.48), residues: 116
  loop : -1.49 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 370 
 TYR   0.017   0.001   TYR C 103 
 PHE   0.011   0.001   PHE J 257 
 TRP   0.011   0.001   TRP J  81 
 HIS   0.003   0.001   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 8852)
  covalent geometry    : angle       0.55323 (11955)
  hydrogen bonds       : bond        0.03939 (  409)
  hydrogen bonds       : angle       4.64585 ( 1131)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: C  434 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7082 (tt0)
REVERT: C  516 MET cc_start: 0.6025 (mpp) cc_final: 0.5529 (mpp)
  outliers start: 16
  outliers final: 7
  residues processed: 75
  average time/residue: 0.0751
  time to fit residues: 7.8485
Evaluate side-chains
  68 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain C residue  184 LYS
Chi-restraints excluded: chain C residue  268 LEU
Chi-restraints excluded: chain C residue  434 GLU
Chi-restraints excluded: chain C residue  450 THR
Chi-restraints excluded: chain C residue  748 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 42 optimal weight:    5.9990
   chunk 75 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 106 optimal weight:    0.0370
   chunk 79 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 68 optimal weight:    0.4980
   chunk 66 optimal weight:    0.0470
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.3956

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

Flipped N/Q/H residues before XYZ refinement:
** C 678 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 = 0.3233 r_free = 0.3233 target = 0.084490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.071118 restraints weight = 18640.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.073065 restraints weight = 10626.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.073390 restraints weight = 7451.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.073676 restraints weight = 6509.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.073874 restraints weight = 5871.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8379
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8852  Z= 0.108
  Angle     :  0.510   6.585  11955  Z= 0.259
  Chirality :  0.042   0.150   1303
  Planarity :  0.003   0.032   1540
  Dihedral  :  5.920  84.730   1186
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.30 %
    Favored  : 88.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.26), residues: 1072
  helix:  1.18 (0.25), residues: 501
  sheet: -0.82 (0.48), residues: 116
  loop : -1.18 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  34 
 TYR   0.017   0.001   TYR C 134 
 PHE   0.010   0.001   PHE C 121 
 TRP   0.028   0.002   TRP C 130 
 HIS   0.003   0.001   HIS J 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 8852)
  covalent geometry    : angle       0.50953 (11955)
  hydrogen bonds       : bond        0.03370 (  409)
  hydrogen bonds       : angle       4.43910 ( 1131)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: C   77 MET cc_start: 0.7494 (mtm) cc_final: 0.7291 (mpp)
REVERT: C  434 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7009 (tt0)
REVERT: C  516 MET cc_start: 0.6027 (mpp) cc_final: 0.5530 (mpp)
  outliers start: 15
  outliers final: 10
  residues processed: 73
  average time/residue: 0.0935
  time to fit residues: 9.1788
Evaluate side-chains
  71 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  154 VAL
Chi-restraints excluded: chain J residue  204 THR
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue   94 THR
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain C residue  184 LYS
Chi-restraints excluded: chain C residue  268 LEU
Chi-restraints excluded: chain C residue  434 GLU
Chi-restraints excluded: chain C residue  450 THR
Chi-restraints excluded: chain C residue  748 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 60 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** C 678 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 = 0.3168 r_free = 0.3168 target = 0.080971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.067490 restraints weight = 18847.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.068928 restraints weight = 10698.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.069178 restraints weight = 8105.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.069552 restraints weight = 7269.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.069733 restraints weight = 6484.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052   8852  Z= 0.274
  Angle     :  0.633   6.148  11955  Z= 0.323
  Chirality :  0.047   0.180   1303
  Planarity :  0.004   0.036   1540
  Dihedral  :  6.514  87.223   1186
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 11.05 %
    Favored  : 87.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.26), residues: 1072
  helix:  0.97 (0.24), residues: 501
  sheet: -0.85 (0.48), residues: 116
  loop : -1.31 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 454 
 TYR   0.021   0.002   TYR C 103 
 PHE   0.014   0.002   PHE J 257 
 TRP   0.013   0.002   TRP J 342 
 HIS   0.005   0.001   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00658 ( 8852)
  covalent geometry    : angle       0.63326 (11955)
  hydrogen bonds       : bond        0.04684 (  409)
  hydrogen bonds       : angle       4.70064 ( 1131)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: C  516 MET cc_start: 0.6079 (mpp) cc_final: 0.5585 (mpp)
  outliers start: 16
  outliers final: 10
  residues processed: 70
  average time/residue: 0.0821
  time to fit residues: 8.0623
Evaluate side-chains
  69 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  192 MET
Chi-restraints excluded: chain J residue  204 THR
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain C residue  184 LYS
Chi-restraints excluded: chain C residue  268 LEU
Chi-restraints excluded: chain C residue  440 MET
Chi-restraints excluded: chain C residue  450 THR
Chi-restraints excluded: chain C residue  748 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 13 optimal weight:    0.5980
   chunk 50 optimal weight:    0.5980
   chunk 88 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 35 optimal weight:    0.3980
   chunk 37 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** C 678 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 = 0.3216 r_free = 0.3216 target = 0.083527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.070148 restraints weight = 18590.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.072133 restraints weight = 10598.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.072458 restraints weight = 7429.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.072638 restraints weight = 6471.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.073061 restraints weight = 5917.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8852  Z= 0.120
  Angle     :  0.526   6.093  11955  Z= 0.267
  Chirality :  0.042   0.146   1303
  Planarity :  0.003   0.033   1540
  Dihedral  :  6.105  85.701   1186
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.91 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.00 (0.26), residues: 1072
  helix:  1.21 (0.25), residues: 502
  sheet: -0.81 (0.48), residues: 116
  loop : -1.13 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  34 
 TYR   0.015   0.001   TYR C 134 
 PHE   0.010   0.001   PHE C 578 
 TRP   0.011   0.001   TRP J  81 
 HIS   0.003   0.001   HIS J 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8852)
  covalent geometry    : angle       0.52639 (11955)
  hydrogen bonds       : bond        0.03579 (  409)
  hydrogen bonds       : angle       4.47310 ( 1131)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: C   77 MET cc_start: 0.7464 (mtm) cc_final: 0.7193 (mpp)
REVERT: C  434 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.6978 (tt0)
REVERT: C  516 MET cc_start: 0.5999 (mpp) cc_final: 0.5520 (mpp)
  outliers start: 12
  outliers final: 10
  residues processed: 68
  average time/residue: 0.0859
  time to fit residues: 8.0416
Evaluate side-chains
  71 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  154 VAL
Chi-restraints excluded: chain J residue  204 THR
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain C residue  184 LYS
Chi-restraints excluded: chain C residue  268 LEU
Chi-restraints excluded: chain C residue  434 GLU
Chi-restraints excluded: chain C residue  450 THR
Chi-restraints excluded: chain C residue  521 CYS
Chi-restraints excluded: chain C residue  748 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 54 optimal weight:    0.5980
   chunk 96 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 87 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 90 optimal weight:    2.9990
   chunk 5 optimal weight:    0.6980
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 373 GLN
** C 678 ASN ** 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 = 0.3206 r_free = 0.3206 target = 0.083025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.069635 restraints weight = 18544.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.071644 restraints weight = 10700.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.071939 restraints weight = 7522.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.072126 restraints weight = 6469.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.072444 restraints weight = 5959.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8852  Z= 0.151
  Angle     :  0.539   5.839  11955  Z= 0.273
  Chirality :  0.043   0.159   1303
  Planarity :  0.003   0.033   1540
  Dihedral  :  6.080  85.139   1186
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.80 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.26), residues: 1072
  helix:  1.27 (0.25), residues: 502
  sheet: -0.81 (0.48), residues: 116
  loop : -1.10 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  34 
 TYR   0.018   0.001   TYR C 134 
 PHE   0.010   0.001   PHE C 578 
 TRP   0.011   0.001   TRP J  81 
 HIS   0.003   0.001   HIS C  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8852)
  covalent geometry    : angle       0.53858 (11955)
  hydrogen bonds       : bond        0.03751 (  409)
  hydrogen bonds       : angle       4.45288 ( 1131)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: C   77 MET cc_start: 0.7452 (mtm) cc_final: 0.7201 (mpp)
REVERT: C  434 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.6994 (tt0)
REVERT: C  516 MET cc_start: 0.6023 (mpp) cc_final: 0.5536 (mpp)
  outliers start: 13
  outliers final: 10
  residues processed: 68
  average time/residue: 0.0719
  time to fit residues: 7.0041
Evaluate side-chains
  70 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  154 VAL
Chi-restraints excluded: chain J residue  204 THR
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain C residue  184 LYS
Chi-restraints excluded: chain C residue  268 LEU
Chi-restraints excluded: chain C residue  434 GLU
Chi-restraints excluded: chain C residue  450 THR
Chi-restraints excluded: chain C residue  521 CYS
Chi-restraints excluded: chain C residue  748 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 104 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9990
   chunk 105 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 102 optimal weight:    0.2980
   chunk 31 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** C 678 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 = 0.3202 r_free = 0.3202 target = 0.082834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.069482 restraints weight = 18482.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.071451 restraints weight = 10708.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.071753 restraints weight = 7547.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.071945 restraints weight = 6475.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.072263 restraints weight = 5970.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8852  Z= 0.161
  Angle     :  0.550   7.194  11955  Z= 0.278
  Chirality :  0.043   0.150   1303
  Planarity :  0.003   0.034   1540
  Dihedral  :  6.099  85.233   1186
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.23 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.26), residues: 1072
  helix:  1.36 (0.25), residues: 495
  sheet: -0.80 (0.48), residues: 116
  loop : -1.06 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  34 
 TYR   0.023   0.001   TYR C 134 
 PHE   0.011   0.001   PHE C 578 
 TRP   0.010   0.001   TRP J  81 
 HIS   0.003   0.001   HIS C 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 8852)
  covalent geometry    : angle       0.54995 (11955)
  hydrogen bonds       : bond        0.03806 (  409)
  hydrogen bonds       : angle       4.46398 ( 1131)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: C   77 MET cc_start: 0.7468 (mtm) cc_final: 0.7206 (mpp)
REVERT: C  434 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.6997 (tt0)
REVERT: C  454 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.6446 (ptt-90)
REVERT: C  516 MET cc_start: 0.6051 (mpp) cc_final: 0.5551 (mpp)
  outliers start: 14
  outliers final: 10
  residues processed: 67
  average time/residue: 0.0896
  time to fit residues: 8.3614
Evaluate side-chains
  71 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  154 VAL
Chi-restraints excluded: chain J residue  204 THR
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue  184 LYS
Chi-restraints excluded: chain C residue  268 LEU
Chi-restraints excluded: chain C residue  434 GLU
Chi-restraints excluded: chain C residue  440 MET
Chi-restraints excluded: chain C residue  450 THR
Chi-restraints excluded: chain C residue  454 ARG
Chi-restraints excluded: chain C residue  521 CYS
Chi-restraints excluded: chain C residue  748 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 88 optimal weight:    0.2980
   chunk 24 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 106 optimal weight:    0.3980
   chunk 35 optimal weight:    0.7980
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** C 678 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 = 0.3214 r_free = 0.3214 target = 0.083491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.070174 restraints weight = 18529.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.072144 restraints weight = 10684.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.072461 restraints weight = 7534.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.072742 restraints weight = 6460.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.072901 restraints weight = 5894.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8852  Z= 0.134
  Angle     :  0.526   7.225  11955  Z= 0.266
  Chirality :  0.042   0.157   1303
  Planarity :  0.003   0.033   1540
  Dihedral  :  5.972  84.644   1186
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.45 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.26), residues: 1072
  helix:  1.43 (0.25), residues: 496
  sheet: -0.78 (0.48), residues: 116
  loop : -1.00 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  34 
 TYR   0.022   0.001   TYR C 134 
 PHE   0.010   0.001   PHE C 578 
 TRP   0.011   0.001   TRP J  81 
 HIS   0.003   0.001   HIS J 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8852)
  covalent geometry    : angle       0.52633 (11955)
  hydrogen bonds       : bond        0.03550 (  409)
  hydrogen bonds       : angle       4.39254 ( 1131)

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: C  134 TYR cc_start: 0.8052 (OUTLIER) cc_final: 0.7709 (m-80)
REVERT: C  387 TYR cc_start: 0.8327 (t80) cc_final: 0.8078 (t80)
REVERT: C  434 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6980 (tt0)
REVERT: C  454 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6423 (ptt-90)
REVERT: C  516 MET cc_start: 0.6042 (mpp) cc_final: 0.5527 (mpp)
  outliers start: 12
  outliers final: 9
  residues processed: 70
  average time/residue: 0.0736
  time to fit residues: 7.2297
Evaluate side-chains
  72 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  154 VAL
Chi-restraints excluded: chain J residue  192 MET
Chi-restraints excluded: chain J residue  204 THR
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue  134 TYR
Chi-restraints excluded: chain C residue  184 LYS
Chi-restraints excluded: chain C residue  268 LEU
Chi-restraints excluded: chain C residue  434 GLU
Chi-restraints excluded: chain C residue  450 THR
Chi-restraints excluded: chain C residue  454 ARG
Chi-restraints excluded: chain C residue  748 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 9 optimal weight:    0.0980
   chunk 48 optimal weight:    0.3980
   chunk 57 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** C 678 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 = 0.3210 r_free = 0.3210 target = 0.083263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.070005 restraints weight = 18437.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.071964 restraints weight = 10417.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.072261 restraints weight = 7401.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.072454 restraints weight = 6419.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.072831 restraints weight = 5856.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.1993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8852  Z= 0.145
  Angle     :  0.539   7.088  11955  Z= 0.271
  Chirality :  0.043   0.157   1303
  Planarity :  0.003   0.033   1540
  Dihedral  :  5.981  84.810   1186
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 12.77 %
    Favored  : 85.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.26), residues: 1072
  helix:  1.44 (0.25), residues: 496
  sheet: -0.76 (0.48), residues: 116
  loop : -0.99 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  34 
 TYR   0.021   0.001   TYR C 134 
 PHE   0.010   0.001   PHE C 578 
 TRP   0.011   0.001   TRP J  81 
 HIS   0.003   0.001   HIS J 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8852)
  covalent geometry    : angle       0.53877 (11955)
  hydrogen bonds       : bond        0.03649 (  409)
  hydrogen bonds       : angle       4.40658 ( 1131)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1092.75 seconds
wall clock time: 19 minutes 41.03 seconds (1181.03 seconds total)