Starting phenix.real_space_refine
on Thu Mar 13 07:34:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ziu_60130/03_2025/8ziu_60130.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ziu_60130/03_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_60130/03_2025/8ziu_60130.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ziu_60130/03_2025/8ziu_60130.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ziu_60130/03_2025/8ziu_60130.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ziu_60130/03_2025/8ziu_60130.cif"
  }
  resolution = 3.54
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.91, per 1000 atoms: 0.80
  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: 2.20
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.01
  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: 2.97

  Time building geometry restraints manager: 2.60 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:             6.590
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.870
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.830
-------------------------------------------------------------------------------
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= 0.274
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.79 (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
 TRP   0.012   0.002   TRP J  81 
 HIS   0.005   0.001   HIS C 153 
 PHE   0.012   0.001   PHE C 489 
 TYR   0.016   0.001   TYR C 103 
 ARG   0.003   0.000   ARG J  30 

*********************** 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  : 0.931 
Fit side-chains
   revert: symmetry clash
REVERT: C   86 LYS cc_start: 0.7631 (ttmm) cc_final: 0.7396 (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: 0.8255 (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: 0.2468
  time to fit residues: 32.1188
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  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 84 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 63 optimal weight:    0.6980
   chunk 98 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 487 GLN
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: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.082973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.069722 restraints weight = 18235.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.070433 restraints weight = 10461.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.070980 restraints weight = 8842.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1173

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= 0.253
  Angle     :  0.586   6.113  11955  Z= 0.303
  Chirality :  0.044   0.181   1303
  Planarity :  0.004   0.034   1540
  Dihedral  :  6.424  87.959   1186
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  6.44 %
    Favored  : 92.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (0.25), residues: 1072
  helix:  0.19 (0.24), residues: 501
  sheet: -1.25 (0.48), residues: 112
  loop : -2.00 (0.25), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 130 
 HIS   0.004   0.001   HIS C 359 
 PHE   0.014   0.001   PHE C 511 
 TYR   0.016   0.001   TYR C 103 
 ARG   0.004   0.000   ARG C 370 

*********************** 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
  80 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
REVERT: C  387 TYR cc_start: 0.8381 (t80) cc_final: 0.8174 (t80)
REVERT: C  434 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7045 (tt0)
REVERT: C  516 MET cc_start: 0.6052 (mpp) cc_final: 0.5567 (mpp)
REVERT: C  569 ASN cc_start: 0.6996 (p0) cc_final: 0.6760 (m-40)
  outliers start: 9
  outliers final: 4
  residues processed: 77
  average time/residue: 0.2286
  time to fit residues: 24.8181
Evaluate side-chains
  66 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
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 11 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0060
   chunk 2 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 23 optimal weight:    0.2980
   chunk 103 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.6398

-------------------------------------------------------------------------------
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 = 0.3209 r_free = 0.3209 target = 0.083207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.069707 restraints weight = 18499.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.071677 restraints weight = 10521.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.071950 restraints weight = 7409.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1443

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= 0.230
  Angle     :  0.557   8.153  11955  Z= 0.285
  Chirality :  0.043   0.153   1303
  Planarity :  0.003   0.033   1540
  Dihedral  :  6.217  86.756   1186
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  7.73 %
    Favored  : 91.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.25), residues: 1072
  helix:  0.77 (0.24), residues: 498
  sheet: -0.93 (0.49), residues: 109
  loop : -1.67 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP J  81 
 HIS   0.003   0.001   HIS C  97 
 PHE   0.011   0.001   PHE C 511 
 TYR   0.017   0.001   TYR C 103 
 ARG   0.003   0.000   ARG C  34 

*********************** 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
  73 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
REVERT: C  387 TYR cc_start: 0.8346 (t80) cc_final: 0.8132 (t80)
REVERT: C  434 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7020 (tt0)
REVERT: C  516 MET cc_start: 0.5960 (mpp) cc_final: 0.5428 (mpp)
  outliers start: 10
  outliers final: 6
  residues processed: 71
  average time/residue: 0.2448
  time to fit residues: 24.0797
Evaluate side-chains
  68 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
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  450 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 40 optimal weight:    0.0870
   chunk 69 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0020
   chunk 76 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    0.6980
   chunk 36 optimal weight:    0.0070
   chunk 5 optimal weight:    0.2980
   chunk 67 optimal weight:    4.9990
   chunk 100 optimal weight:    0.6980
   chunk 30 optimal weight:    0.3980
   overall best weight:    0.1584

-------------------------------------------------------------------------------
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 = 0.3256 r_free = 0.3256 target = 0.085791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.072533 restraints weight = 18308.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.074373 restraints weight = 10432.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.074693 restraints weight = 7459.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
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      :  0.002   0.035   8852  Z= 0.120
  Angle     :  0.489   6.959  11955  Z= 0.250
  Chirality :  0.041   0.139   1303
  Planarity :  0.003   0.032   1540
  Dihedral  :  5.752  84.038   1186
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.12 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.26), residues: 1072
  helix:  1.10 (0.25), residues: 504
  sheet: -0.82 (0.49), residues: 115
  loop : -1.31 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP J  81 
 HIS   0.003   0.000   HIS J 163 
 PHE   0.010   0.001   PHE C 121 
 TYR   0.017   0.001   TYR C 134 
 ARG   0.005   0.000   ARG C 370 

*********************** 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
  79 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
REVERT: C  387 TYR cc_start: 0.8250 (t80) cc_final: 0.7980 (t80)
REVERT: C  434 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.6983 (tt0)
REVERT: C  516 MET cc_start: 0.6068 (mpp) cc_final: 0.5571 (mpp)
REVERT: C  569 ASN cc_start: 0.6992 (p0) cc_final: 0.6740 (m-40)
  outliers start: 12
  outliers final: 6
  residues processed: 76
  average time/residue: 0.2249
  time to fit residues: 23.8732
Evaluate side-chains
  68 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue  154 VAL
Chi-restraints excluded: chain C residue   35 THR
Chi-restraints excluded: chain C residue   94 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
Chi-restraints excluded: chain C residue  450 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 77 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 66 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 103 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.083050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.069688 restraints weight = 18530.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.071544 restraints weight = 10483.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.071869 restraints weight = 7437.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8852  Z= 0.262
  Angle     :  0.548   6.019  11955  Z= 0.278
  Chirality :  0.043   0.148   1303
  Planarity :  0.003   0.035   1540
  Dihedral  :  5.961  84.606   1186
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 10.09 %
    Favored  : 88.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.26), residues: 1072
  helix:  1.11 (0.25), residues: 505
  sheet: -0.75 (0.50), residues: 109
  loop : -1.26 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C 130 
 HIS   0.004   0.001   HIS C  97 
 PHE   0.011   0.001   PHE J 257 
 TYR   0.018   0.001   TYR C 103 
 ARG   0.003   0.000   ARG C  34 

*********************** 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
  76 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
REVERT: C  387 TYR cc_start: 0.8300 (t80) cc_final: 0.8041 (t80)
REVERT: C  434 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7065 (tt0)
REVERT: C  516 MET cc_start: 0.6073 (mpp) cc_final: 0.5573 (mpp)
  outliers start: 15
  outliers final: 11
  residues processed: 71
  average time/residue: 0.2515
  time to fit residues: 24.9194
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  : 0.905 
-------------------------------------------------------------------------------
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  440 MET
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 35 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 8 optimal weight:    0.3980
   chunk 87 optimal weight:    0.0980
   chunk 80 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3197 r_free = 0.3197 target = 0.082460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.069040 restraints weight = 18473.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.071054 restraints weight = 10716.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.071340 restraints weight = 7484.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8431
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8852  Z= 0.285
  Angle     :  0.559   6.041  11955  Z= 0.284
  Chirality :  0.044   0.154   1303
  Planarity :  0.004   0.036   1540
  Dihedral  :  6.152  85.260   1186
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 10.09 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.26), residues: 1072
  helix:  1.10 (0.24), residues: 505
  sheet: -0.79 (0.49), residues: 111
  loop : -1.20 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 130 
 HIS   0.004   0.001   HIS C  97 
 PHE   0.011   0.001   PHE C 578 
 TYR   0.017   0.001   TYR C 103 
 ARG   0.003   0.000   ARG C  34 

*********************** 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
  78 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 2.953 
Fit side-chains
   revert: symmetry clash
REVERT: C  387 TYR cc_start: 0.8316 (t80) cc_final: 0.8076 (t80)
REVERT: C  434 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7111 (tt0)
REVERT: C  516 MET cc_start: 0.6130 (mpp) cc_final: 0.5630 (mpp)
  outliers start: 17
  outliers final: 11
  residues processed: 73
  average time/residue: 0.4464
  time to fit residues: 47.3224
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  : 1.219 
-------------------------------------------------------------------------------
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  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 94 optimal weight:    0.0870
   chunk 59 optimal weight:    0.9980
   chunk 71 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 82 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 79 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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 = 0.3213 r_free = 0.3213 target = 0.083325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.069949 restraints weight = 18685.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.071871 restraints weight = 10606.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.072177 restraints weight = 7478.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.1834

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= 0.222
  Angle     :  0.532   6.072  11955  Z= 0.270
  Chirality :  0.043   0.152   1303
  Planarity :  0.003   0.036   1540
  Dihedral  :  6.045  84.793   1186
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 10.73 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.26), residues: 1072
  helix:  1.33 (0.25), residues: 496
  sheet: -0.83 (0.48), residues: 116
  loop : -1.12 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP J  81 
 HIS   0.003   0.001   HIS C  97 
 PHE   0.010   0.001   PHE C 578 
 TYR   0.015   0.001   TYR C 134 
 ARG   0.003   0.000   ARG C  34 

*********************** 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
  80 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
REVERT: C  387 TYR cc_start: 0.8314 (t80) cc_final: 0.8077 (t80)
REVERT: C  434 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7079 (tt0)
REVERT: C  516 MET cc_start: 0.6121 (mpp) cc_final: 0.5623 (mpp)
  outliers start: 17
  outliers final: 12
  residues processed: 74
  average time/residue: 0.2556
  time to fit residues: 26.1029
Evaluate side-chains
  74 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
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  440 MET
Chi-restraints excluded: chain C residue  450 THR
Chi-restraints excluded: chain C residue  612 LYS
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 25 optimal weight:    0.6980
   chunk 99 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 38 optimal weight:    0.4980
   chunk 64 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 28 optimal weight:    0.4980
   chunk 88 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   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 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 = 0.3209 r_free = 0.3209 target = 0.083121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.069787 restraints weight = 18758.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.071705 restraints weight = 10610.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.072029 restraints weight = 7436.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1876

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= 0.233
  Angle     :  0.539   5.932  11955  Z= 0.273
  Chirality :  0.043   0.157   1303
  Planarity :  0.003   0.033   1540
  Dihedral  :  6.046  84.775   1186
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.16 %
    Favored  : 87.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.26), residues: 1072
  helix:  1.36 (0.25), residues: 496
  sheet: -0.79 (0.48), residues: 116
  loop : -1.09 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP J  81 
 HIS   0.003   0.001   HIS C  97 
 PHE   0.011   0.001   PHE C 578 
 TYR   0.016   0.001   TYR C 103 
 ARG   0.003   0.000   ARG C 370 

*********************** 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
  76 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: C   77 MET cc_start: 0.7527 (mtm) cc_final: 0.7178 (mpp)
REVERT: C  387 TYR cc_start: 0.8301 (t80) cc_final: 0.8046 (t80)
REVERT: C  434 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7067 (tt0)
REVERT: C  516 MET cc_start: 0.6122 (mpp) cc_final: 0.5590 (mpp)
  outliers start: 13
  outliers final: 12
  residues processed: 70
  average time/residue: 0.2368
  time to fit residues: 23.2850
Evaluate side-chains
  74 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
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  440 MET
Chi-restraints excluded: chain C residue  450 THR
Chi-restraints excluded: chain C residue  612 LYS
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 12 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   chunk 55 optimal weight:    0.2980
   chunk 43 optimal weight:    1.9990
   chunk 101 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 99 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   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 = 0.3213 r_free = 0.3213 target = 0.083257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.069981 restraints weight = 18489.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.071982 restraints weight = 10605.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.072262 restraints weight = 7446.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.1940

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= 0.221
  Angle     :  0.532   6.102  11955  Z= 0.269
  Chirality :  0.043   0.153   1303
  Planarity :  0.003   0.033   1540
  Dihedral  :  6.001  84.540   1186
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 11.05 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.26), residues: 1072
  helix:  1.41 (0.25), residues: 496
  sheet: -0.77 (0.48), residues: 116
  loop : -1.04 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP J  81 
 HIS   0.003   0.001   HIS C  97 
 PHE   0.010   0.001   PHE C 578 
 TYR   0.018   0.001   TYR C 134 
 ARG   0.004   0.000   ARG C 370 

*********************** 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
  79 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: C   77 MET cc_start: 0.7530 (mtm) cc_final: 0.7180 (mpp)
REVERT: C  387 TYR cc_start: 0.8294 (t80) cc_final: 0.8069 (t80)
REVERT: C  434 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7048 (tt0)
REVERT: C  516 MET cc_start: 0.6120 (mpp) cc_final: 0.5618 (mpp)
  outliers start: 15
  outliers final: 12
  residues processed: 73
  average time/residue: 0.2358
  time to fit residues: 24.1316
Evaluate side-chains
  74 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
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  440 MET
Chi-restraints excluded: chain C residue  450 THR
Chi-restraints excluded: chain C residue  612 LYS
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 6 optimal weight:    0.2980
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 26 optimal weight:    0.0060
   chunk 18 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.4796

-------------------------------------------------------------------------------
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 = 0.3220 r_free = 0.3220 target = 0.083723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.070531 restraints weight = 18554.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.072462 restraints weight = 10407.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.072767 restraints weight = 7363.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.2034

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= 0.182
  Angle     :  0.518   6.024  11955  Z= 0.262
  Chirality :  0.042   0.150   1303
  Planarity :  0.003   0.033   1540
  Dihedral  :  5.885  84.036   1186
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.48 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.26), residues: 1072
  helix:  1.56 (0.25), residues: 490
  sheet: -0.78 (0.47), residues: 122
  loop : -1.01 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP J  81 
 HIS   0.003   0.001   HIS J 163 
 PHE   0.010   0.001   PHE C 578 
 TYR   0.022   0.001   TYR C 134 
 ARG   0.004   0.000   ARG C 370 

********************** 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  : 0.951 
Fit side-chains
   revert: symmetry clash
REVERT: C   77 MET cc_start: 0.7632 (mtm) cc_final: 0.7272 (mpp)
REVERT: C  134 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7610 (m-80)
REVERT: C  387 TYR cc_start: 0.8273 (t80) cc_final: 0.8042 (t80)
REVERT: C  434 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7040 (tt0)
REVERT: C  516 MET cc_start: 0.6122 (mpp) cc_final: 0.5598 (mpp)
  outliers start: 12
  outliers final: 9
  residues processed: 70
  average time/residue: 0.2228
  time to fit residues: 22.1051
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  : 0.950 
-------------------------------------------------------------------------------
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  748 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 103 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0270
   chunk 59 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 95 optimal weight:    0.3980
   chunk 99 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 93 optimal weight:    0.0980
   overall best weight:    0.3438

-------------------------------------------------------------------------------
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 = 0.3239 r_free = 0.3239 target = 0.084797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.071584 restraints weight = 18536.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.073655 restraints weight = 10501.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.073924 restraints weight = 7278.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.2202

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= 0.150
  Angle     :  0.496   5.864  11955  Z= 0.250
  Chirality :  0.041   0.144   1303
  Planarity :  0.003   0.032   1540
  Dihedral  :  5.665  82.875   1186
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.80 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.27), residues: 1072
  helix:  1.70 (0.25), residues: 489
  sheet: -0.67 (0.47), residues: 122
  loop : -0.89 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP J  81 
 HIS   0.003   0.001   HIS J 163 
 PHE   0.009   0.001   PHE C 578 
 TYR   0.020   0.001   TYR C 134 
 ARG   0.004   0.000   ARG C 370 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2663.44 seconds
wall clock time: 48 minutes 4.06 seconds (2884.06 seconds total)