Starting phenix.real_space_refine
on Wed Aug  5 05:37:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zip_60125/08_2026/8zip_60125.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zip_60125/08_2026/8zip_60125.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zip_60125/08_2026/8zip_60125.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zip_60125/08_2026/8zip_60125.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zip_60125/08_2026/8zip_60125.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zip_60125/08_2026/8zip_60125.map"
  }
  resolution = 4.9
  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    5511      2.51       5
     N    1465      2.21       5
     O    1632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 8662
  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: 5748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 714, 5748
          Classifications: {'peptide': 714}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 24, 'TRANS': 687}
          Chain breaks: 6
    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: 1.91, per 1000 atoms: 0.22
  Number of scatterers: 8662
  At special positions: 0
  Unit cell: (127.82, 95.45, 112.88, 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    1632      8.00
     N    1465      7.00
     C    5511      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 335.8 milliseconds
  

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2028

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 13 sheets defined
      51.2% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  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
      removed outlier: 3.639A  pdb=" N   HIS J 103 " --> pdb=" O   PRO J 100 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 114 through 129
      removed outlier: 4.175A  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
      removed outlier: 3.703A  pdb=" N   ILE J 177 " --> pdb=" O   PRO J 174 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 174 through 177'
    Processing helix  chain 'J' and resid 183 through 195
    Processing helix  chain 'J' and resid 196 through 199
    Processing helix  chain 'J' and resid 204 through 219
      removed outlier: 3.538A  pdb=" N   CYS J 219 " --> pdb=" O   LYS J 215 " (cutoff:3.500A)
    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: 3.537A  pdb=" N   ILE J 269 " --> pdb=" O   PRO J 266 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 275 through 286
    Processing helix  chain 'J' and resid 291 through 296
    Processing helix  chain 'J' and resid 303 through 307
    Processing helix  chain 'J' and resid 310 through 323
    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 376
    Processing helix  chain 'C' and resid 6 through 11
      removed outlier: 6.927A  pdb=" N   ALA C  11 " --> pdb=" O   ASP C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 17
    Processing helix  chain 'C' and resid 19 through 27
      removed outlier: 3.695A  pdb=" N   ARG C  23 " --> pdb=" O   SER C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 85
      removed outlier: 3.710A  pdb=" N   ASP C  85 " --> pdb=" O   PRO C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 93
      removed outlier: 3.578A  pdb=" N   MET C  92 " --> pdb=" O   ASP C  89 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU C  93 " --> pdb=" O   MET C  90 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 89 through 93'
    Processing helix  chain 'C' and resid 97 through 111
    Processing helix  chain 'C' and resid 136 through 141
      removed outlier: 3.753A  pdb=" N   ALA C 140 " --> pdb=" O   ALA C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 169
    Processing helix  chain 'C' and resid 183 through 199
    Processing helix  chain 'C' and resid 216 through 232
      removed outlier: 3.867A  pdb=" N   ALA C 224 " --> pdb=" O   GLN C 220 " (cutoff:3.500A)
      Proline residue:  C 226  - end of helix
    Processing helix  chain 'C' and resid 271 through 275
    Processing helix  chain 'C' and resid 284 through 292
      removed outlier: 4.475A  pdb=" N   TYR C 288 " --> pdb=" O   TYR C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 302
      removed outlier: 3.724A  pdb=" N   LEU C 299 " --> pdb=" O   LYS C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 311
      removed outlier: 3.585A  pdb=" N   ASP C 310 " --> pdb=" O   ASN C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 326 through 340
    Processing helix  chain 'C' and resid 344 through 361
      removed outlier: 4.896A  pdb=" N   VAL C 350 " --> pdb=" O   GLU C 346 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLY C 361 " --> pdb=" O   ILE C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 379 through 390
    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 516 through 521
      removed outlier: 4.051A  pdb=" N   CYS C 521 " --> pdb=" O   ASP C 517 " (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
    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: 3.759A  pdb=" N   THR C 666 " --> pdb=" O   THR C 662 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 687 through 699
    Processing helix  chain 'C' and resid 699 through 708
    Processing helix  chain 'C' and resid 716 through 724
      removed outlier: 4.052A  pdb=" N   PHE C 720 " --> pdb=" O   LEU C 716 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 744 through 750
    Processing sheet with id=AA1, first strand: chain 'J' and resid 31 through 34
      removed outlier: 6.870A  pdb=" N   LEU J  10 " --> pdb=" O   LEU J 106 " (cutoff:3.500A)
      removed outlier: 8.355A  pdb=" N   THR J 108 " --> pdb=" O   LEU J  10 " (cutoff:3.500A)
      removed outlier: 8.115A  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: 6.369A  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 244
      removed outlier: 3.704A  pdb=" N   LEU J 244 " --> pdb=" O   GLN J 248 " (cutoff:3.500A)
      removed outlier: 5.256A  pdb=" N   GLN J 248 " --> pdb=" O   LEU J 244 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 49
    Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 64
    Processing sheet with id=AA8, first strand: chain 'C' and resid 115 through 118
      removed outlier: 3.559A  pdb=" N   SER C 118 " --> pdb=" O   PHE C 121 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   CYS C 122 " --> pdb=" O   ARG C 673 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   ILE C 675 " --> pdb=" O   CYS C 122 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   THR C 124 " --> pdb=" O   ILE C 675 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   SER C 173 " --> pdb=" O   HIS C 670 " (cutoff:3.500A)
      removed outlier: 7.390A  pdb=" N   VAL C 672 " --> pdb=" O   SER C 173 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   LEU C 175 " --> pdb=" O   VAL C 672 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   CYS C 674 " --> pdb=" O   LEU C 175 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   THR C 177 " --> pdb=" O   CYS C 674 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   GLN C 172 " --> pdb=" O   GLY C 459 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   LEU C 461 " --> pdb=" O   GLN C 172 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   ILE C 174 " --> pdb=" O   LEU C 461 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   ILE C 463 " --> pdb=" O   ILE C 174 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE C 176 " --> pdb=" O   ILE C 463 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   GLY C 246 " --> pdb=" O   THR C 266 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   THR C 266 " --> pdb=" O   GLY C 246 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   PHE C 248 " --> pdb=" O   ILE C 264 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   ILE C 264 " --> pdb=" O   PHE C 248 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ARG C 250 " --> pdb=" O   ALA C 262 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   ALA C 262 " --> pdb=" O   ARG C 250 " (cutoff:3.500A)
      removed outlier: 4.378A  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
      removed outlier: 3.608A  pdb=" N   ALA C 234 " --> pdb=" O   SER C 242 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER C 242 " --> pdb=" O   ALA C 234 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    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
      removed outlier: 3.566A  pdb=" N   VAL C 412 " --> pdb=" O   VAL C 405 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 564 through 565
      removed outlier: 3.654A  pdb=" N   PHE C 578 " --> pdb=" O   TYR C 589 " (cutoff:3.500A)
      removed outlier: 3.946A  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: 1.34

  Time building geometry restraints manager: 1.11 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: 2815
        1.34 -     1.46: 1599
        1.46 -     1.58: 4338
        1.58 -     1.69: 3
        1.69 -     1.81: 90
  Bond restraints: 8845
  Sorted by residual:
  bond pdb=" N   GLU C 410 "
       pdb=" CA  GLU C 410 "
    ideal  model  delta    sigma   weight residual
    1.455  1.484 -0.029 1.25e-02 6.40e+03 5.38e+00
  bond pdb=" C   GLN C 452 "
       pdb=" N   PRO C 453 "
    ideal  model  delta    sigma   weight residual
    1.331  1.353 -0.022 1.20e-02 6.94e+03 3.33e+00
  bond pdb=" C   GLN J 265 "
       pdb=" N   PRO J 266 "
    ideal  model  delta    sigma   weight residual
    1.337  1.319  0.018 9.80e-03 1.04e+04 3.19e+00
  bond pdb=" C4  ADP J 401 "
       pdb=" C5  ADP J 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.457  0.033 2.00e-02 2.50e+03 2.67e+00
  bond pdb=" CB  ARG J  64 "
       pdb=" CG  ARG J  64 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 3.00e-02 1.11e+03 2.52e+00
  ... (remaining 8840 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 11630
        1.80 -     3.59: 273
        3.59 -     5.39: 32
        5.39 -     7.19: 6
        7.19 -     8.98: 2
  Bond angle restraints: 11943
  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
     114.85  107.98    6.87 1.35e+00 5.49e-01 2.59e+01
  angle pdb=" C   GLY C 710 "
        pdb=" N   PHE C 711 "
        pdb=" CA  PHE C 711 "
      ideal   model   delta    sigma   weight residual
     121.70  127.94   -6.24 1.80e+00 3.09e-01 1.20e+01
  angle pdb=" N   ASN C 688 "
        pdb=" CA  ASN C 688 "
        pdb=" C   ASN C 688 "
      ideal   model   delta    sigma   weight residual
     109.81  117.31   -7.50 2.21e+00 2.05e-01 1.15e+01
  angle pdb=" CA  GLY C 710 "
        pdb=" C   GLY C 710 "
        pdb=" N   PHE C 711 "
      ideal   model   delta    sigma   weight residual
     115.50  120.35   -4.85 1.45e+00 4.76e-01 1.12e+01
  angle pdb=" N   PHE C 711 "
        pdb=" CA  PHE C 711 "
        pdb=" C   PHE C 711 "
      ideal   model   delta    sigma   weight residual
     111.00  119.98   -8.98 2.80e+00 1.28e-01 1.03e+01
  ... (remaining 11938 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.62: 4968
       21.62 -    43.25: 311
       43.25 -    64.87: 36
       64.87 -    86.49: 13
       86.49 -   108.12: 4
  Dihedral angle restraints: 5332
    sinusoidal: 2179
      harmonic: 3153
  Sorted by residual:
  dihedral pdb=" C5' ADP J 401 "
           pdb=" O5' ADP J 401 "
           pdb=" PA  ADP J 401 "
           pdb=" O2A ADP J 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   48.12 -108.12     1      2.00e+01 2.50e-03 3.15e+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 -153.24  -26.76     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  ASP J 181 "
           pdb=" C   ASP J 181 "
           pdb=" N   LEU J 182 "
           pdb=" CA  LEU J 182 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.70   19.30     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 5329 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 942
       0.047 -    0.094: 288
       0.094 -    0.141: 69
       0.141 -    0.188: 2
       0.188 -    0.235: 1
  Chirality restraints: 1302
  Sorted by residual:
  chirality pdb=" CA  ASN C 688 "
            pdb=" N   ASN C 688 "
            pdb=" C   ASN C 688 "
            pdb=" CB  ASN C 688 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  PHE C 711 "
            pdb=" N   PHE C 711 "
            pdb=" C   PHE C 711 "
            pdb=" CB  PHE C 711 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.55e-01
  chirality pdb=" CA  PRO J 114 "
            pdb=" N   PRO J 114 "
            pdb=" C   PRO J 114 "
            pdb=" CB  PRO J 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.14 2.00e-01 2.50e+01 5.23e-01
  ... (remaining 1299 not shown)

  Planarity restraints: 1537
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C  98 "    0.034 5.00e-02 4.00e+02   5.08e-02 4.13e+00
        pdb=" N   PRO C  99 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO C  99 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C  99 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 225 "   -0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO C 226 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO C 226 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 226 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 409 "    0.008 2.00e-02 2.50e+03   1.53e-02 2.34e+00
        pdb=" C   ASN C 409 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ASN C 409 "    0.010 2.00e-02 2.50e+03
        pdb=" N   GLU C 410 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1534 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     2.09: 2
        2.09 -     2.79: 2259
        2.79 -     3.49: 12294
        3.49 -     4.20: 20711
        4.20 -     4.90: 36440
  Nonbonded interactions: 71706
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP J  27 "
            pdb=" OG  SER C 644 "
     model   vdw
     1.384 3.040
  nonbonded pdb=" N   THR J 353 "
            pdb=" OE2 GLU C 537 "
     model   vdw
     1.995 3.120
  nonbonded pdb=" O   HIS C 153 "
            pdb=" OG  SER C 156 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" O   MET C 389 "
            pdb=" OG  SER C 613 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OD1 ASP J 159 "
            pdb=" O3' ADP J 401 "
     model   vdw
     2.183 3.040
  ... (remaining 71701 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:             9.990
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.520
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7154
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      :  0.006   0.058   8846  Z= 0.272
  Angle     :  0.694   8.983  11943  Z= 0.395
  Chirality :  0.045   0.235   1302
  Planarity :  0.004   0.051   1537
  Dihedral  : 14.309 108.115   3304
  Min Nonbonded Distance : 1.384

Molprobity Statistics.
  All-atom Clashscore : 15.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.13 (0.22), residues: 1069
  helix: -1.51 (0.21), residues: 471
  sheet: -2.31 (0.43), residues: 132
  loop : -2.52 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG J 258 
 TYR   0.013   0.001   TYR C 311 
 PHE   0.016   0.002   PHE C 253 
 TRP   0.016   0.002   TRP J 342 
 HIS   0.010   0.001   HIS C 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00613 /  0.27 ( 8845)
  covalent geometry    : angle       0.69355 /  0.39 (11943)
  hydrogen bonds       : bond        0.18014 / 12.61 (  409)
  hydrogen bonds       : angle       7.04546 /  4.92 ( 1131)
  Misc. bond           : bond        0.00103 /  0.05 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   26 ASP cc_start: 0.8233 (m-30) cc_final: 0.7677 (t0)
REVERT: J  113 ASN cc_start: 0.7586 (p0) cc_final: 0.7327 (p0)
REVERT: J  159 ASP cc_start: 0.5642 (t70) cc_final: 0.4378 (t70)
REVERT: J  218 LEU cc_start: 0.9000 (mt) cc_final: 0.8765 (tp)
REVERT: J  252 ILE cc_start: 0.8075 (pt) cc_final: 0.7623 (mm)
REVERT: J  300 VAL cc_start: 0.8962 (t) cc_final: 0.8207 (t)
REVERT: J  347 ILE cc_start: 0.8946 (mt) cc_final: 0.8732 (mm)
REVERT: C   75 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8286 (tm-30)
REVERT: C   77 MET cc_start: 0.7941 (mpp) cc_final: 0.7735 (mpp)
REVERT: C  113 MET cc_start: 0.7662 (mtp) cc_final: 0.7318 (mtt)
REVERT: C  290 ILE cc_start: 0.9520 (mt) cc_final: 0.9304 (tp)
REVERT: C  358 MET cc_start: 0.8844 (mtm) cc_final: 0.8590 (mtp)
REVERT: C  363 MET cc_start: 0.9113 (mtp) cc_final: 0.8892 (tpp)
REVERT: C  489 PHE cc_start: 0.9032 (t80) cc_final: 0.8798 (t80)
REVERT: C  517 ASP cc_start: 0.8857 (m-30) cc_final: 0.8554 (t0)
REVERT: C  547 MET cc_start: 0.9090 (tmm) cc_final: 0.8814 (tmm)
REVERT: C  687 ASP cc_start: 0.8803 (m-30) cc_final: 0.8570 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.1022
  time to fit residues: 24.0128
Evaluate side-chains
  105 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.4503 > 50:)
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0070
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    0.3980
   chunk 106 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.6198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
J  14 ASN
J  75 HIS
J 175 HIS
J 355 GLN
** C  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 223 GLN
C 285 HIS
C 487 GLN
C 488 GLN
C 493 HIS
C 556 ASN
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 658 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.046261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.038368 restraints weight = 74129.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.039586 restraints weight = 48620.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.040502 restraints weight = 35025.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.041193 restraints weight = 26779.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.041657 restraints weight = 21432.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8846  Z= 0.134
  Angle     :  0.636   8.786  11943  Z= 0.335
  Chirality :  0.044   0.236   1302
  Planarity :  0.004   0.061   1537
  Dihedral  :  6.032  74.363   1185
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.25), residues: 1069
  helix: -0.06 (0.23), residues: 478
  sheet: -1.73 (0.41), residues: 146
  loop : -1.65 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG J  30 
 TYR   0.014   0.001   TYR C 456 
 PHE   0.019   0.001   PHE C 671 
 TRP   0.013   0.001   TRP J  81 
 HIS   0.009   0.001   HIS J 373 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 8845)
  covalent geometry    : angle       0.63643 /  0.34 (11943)
  hydrogen bonds       : bond        0.04094 /  2.76 (  409)
  hydrogen bonds       : angle       5.62560 /  3.93 ( 1131)
  Misc. bond           : bond        0.00361 /  0.19 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   49 MET cc_start: 0.3918 (ptt) cc_final: 0.3623 (ptp)
REVERT: J  117 ASN cc_start: 0.8948 (t0) cc_final: 0.8548 (t0)
REVERT: J  125 MET cc_start: 0.8919 (mmm) cc_final: 0.8532 (mtt)
REVERT: J  128 THR cc_start: 0.8946 (t) cc_final: 0.8163 (t)
REVERT: J  134 MET cc_start: 0.8006 (tmm) cc_final: 0.7673 (tmm)
REVERT: J  271 MET cc_start: 0.6935 (tpt) cc_final: 0.6469 (tpt)
REVERT: J  294 ASP cc_start: 0.9407 (m-30) cc_final: 0.8912 (m-30)
REVERT: J  337 ARG cc_start: 0.7874 (ptt-90) cc_final: 0.7547 (ptp90)
REVERT: C  113 MET cc_start: 0.7815 (mtp) cc_final: 0.7172 (mtt)
REVERT: C  267 TYR cc_start: 0.7033 (m-80) cc_final: 0.6673 (m-80)
REVERT: C  363 MET cc_start: 0.9152 (mtp) cc_final: 0.8941 (tpp)
REVERT: C  389 MET cc_start: 0.8523 (mpp) cc_final: 0.8275 (mpp)
REVERT: C  486 LEU cc_start: 0.9279 (mt) cc_final: 0.8876 (tt)
REVERT: C  517 ASP cc_start: 0.9054 (m-30) cc_final: 0.8655 (t0)
REVERT: C  547 MET cc_start: 0.9222 (tmm) cc_final: 0.8821 (tmm)
REVERT: C  575 GLU cc_start: 0.8933 (pt0) cc_final: 0.8460 (pp20)
REVERT: C  581 VAL cc_start: 0.8945 (t) cc_final: 0.8478 (t)
REVERT: C  767 PHE cc_start: 0.7574 (m-80) cc_final: 0.7366 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0839
  time to fit residues: 15.2708
Evaluate side-chains
  89 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 52 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 43 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 37 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 42 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
J 175 HIS
J 299 ASN
C 293 ASN
C 402 HIS
** C 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 663 ASN
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.044642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.037002 restraints weight = 78100.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.038158 restraints weight = 51011.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.039016 restraints weight = 36657.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.039666 restraints weight = 28032.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.040175 restraints weight = 22510.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8846  Z= 0.189
  Angle     :  0.681   8.786  11943  Z= 0.357
  Chirality :  0.044   0.223   1302
  Planarity :  0.004   0.062   1537
  Dihedral  :  5.780  47.636   1185
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 15.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.44 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.25), residues: 1069
  helix:  0.26 (0.24), residues: 482
  sheet: -1.50 (0.42), residues: 141
  loop : -1.37 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 244 
 TYR   0.015   0.001   TYR C 288 
 PHE   0.012   0.001   PHE C 541 
 TRP   0.014   0.002   TRP J  81 
 HIS   0.007   0.002   HIS J  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00406 /  0.19 ( 8845)
  covalent geometry    : angle       0.68115 /  0.36 (11943)
  hydrogen bonds       : bond        0.04085 /  2.77 (  409)
  hydrogen bonds       : angle       5.66191 /  3.96 ( 1131)
  Misc. bond           : bond        0.00330 /  0.17 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   46 MET cc_start: 0.6142 (ptp) cc_final: 0.5766 (ptp)
REVERT: J  125 MET cc_start: 0.9076 (mmm) cc_final: 0.8849 (mtt)
REVERT: J  134 MET cc_start: 0.7923 (tmm) cc_final: 0.7705 (tmm)
REVERT: J  167 ILE cc_start: 0.8932 (mm) cc_final: 0.8716 (mm)
REVERT: J  192 MET cc_start: 0.9022 (ttm) cc_final: 0.8669 (tpt)
REVERT: J  242 TYR cc_start: 0.7979 (t80) cc_final: 0.7398 (t80)
REVERT: J  271 MET cc_start: 0.7230 (tpt) cc_final: 0.6661 (tpt)
REVERT: J  294 ASP cc_start: 0.9205 (m-30) cc_final: 0.8966 (m-30)
REVERT: C    6 MET cc_start: 0.8430 (mtp) cc_final: 0.8222 (mtp)
REVERT: C   77 MET cc_start: 0.7937 (mpp) cc_final: 0.7665 (mpp)
REVERT: C  113 MET cc_start: 0.7638 (mtp) cc_final: 0.6960 (mtt)
REVERT: C  389 MET cc_start: 0.8489 (mpp) cc_final: 0.8239 (mpp)
REVERT: C  486 LEU cc_start: 0.9246 (mt) cc_final: 0.8848 (tt)
REVERT: C  517 ASP cc_start: 0.9075 (m-30) cc_final: 0.8708 (t0)
REVERT: C  547 MET cc_start: 0.9202 (tmm) cc_final: 0.8806 (tmm)
REVERT: C  575 GLU cc_start: 0.8934 (pt0) cc_final: 0.8483 (pp20)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 0.0824
  time to fit residues: 12.7288
Evaluate side-chains
  79 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 72 optimal weight:    4.9990
   chunk 69 optimal weight:    0.6980
   chunk 37 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0020
   chunk 102 optimal weight:    0.8980
   chunk 106 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0050
   overall best weight:    0.4402

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
J 356 GLN
** C 569 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 = 0.3120 r_free = 0.3120 target = 0.045947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.038130 restraints weight = 76641.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.039297 restraints weight = 50548.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2928 r_free = 0.2928 target = 0.040188 restraints weight = 36599.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.040832 restraints weight = 28072.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.041371 restraints weight = 22717.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8846  Z= 0.107
  Angle     :  0.592   8.653  11943  Z= 0.304
  Chirality :  0.042   0.212   1302
  Planarity :  0.004   0.059   1537
  Dihedral  :  5.363  42.701   1185
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.51 (0.26), residues: 1069
  helix:  0.69 (0.24), residues: 486
  sheet: -1.27 (0.43), residues: 141
  loop : -1.10 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG J  30 
 TYR   0.013   0.001   TYR C 288 
 PHE   0.014   0.001   PHE C 490 
 TRP   0.012   0.001   TRP J  81 
 HIS   0.005   0.001   HIS C 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 8845)
  covalent geometry    : angle       0.59223 /  0.30 (11943)
  hydrogen bonds       : bond        0.03341 /  2.25 (  409)
  hydrogen bonds       : angle       5.17571 /  3.59 ( 1131)
  Misc. bond           : bond        0.00178 /  0.09 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   46 MET cc_start: 0.6765 (ptp) cc_final: 0.6354 (ptp)
REVERT: J  125 MET cc_start: 0.8942 (mmm) cc_final: 0.8659 (ttm)
REVERT: J  192 MET cc_start: 0.9046 (ttm) cc_final: 0.8738 (tpp)
REVERT: J  242 TYR cc_start: 0.7939 (t80) cc_final: 0.7336 (t80)
REVERT: J  271 MET cc_start: 0.7100 (tpt) cc_final: 0.6585 (tpt)
REVERT: J  294 ASP cc_start: 0.9236 (m-30) cc_final: 0.9023 (m-30)
REVERT: J  307 MET cc_start: 0.7851 (mmp) cc_final: 0.7422 (mmm)
REVERT: C    6 MET cc_start: 0.8556 (mtp) cc_final: 0.8158 (mtp)
REVERT: C  113 MET cc_start: 0.7702 (mtp) cc_final: 0.7038 (mtt)
REVERT: C  389 MET cc_start: 0.8364 (mpp) cc_final: 0.8135 (mpp)
REVERT: C  486 LEU cc_start: 0.9174 (mt) cc_final: 0.8761 (tt)
REVERT: C  517 ASP cc_start: 0.9002 (m-30) cc_final: 0.8709 (t0)
REVERT: C  575 GLU cc_start: 0.8956 (pt0) cc_final: 0.8423 (pp20)
REVERT: C  581 VAL cc_start: 0.8834 (t) cc_final: 0.8417 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0757
  time to fit residues: 12.6475
Evaluate side-chains
  79 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   chunk 107 optimal weight:    7.9990
   chunk 78 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
J  42 HIS
J 362 GLN
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 693 HIS
C 755 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.044279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.036763 restraints weight = 81268.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.037853 restraints weight = 54196.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.038674 restraints weight = 39594.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.039303 restraints weight = 30599.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.039780 restraints weight = 24781.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8846  Z= 0.204
  Angle     :  0.680   8.338  11943  Z= 0.354
  Chirality :  0.044   0.247   1302
  Planarity :  0.005   0.056   1537
  Dihedral  :  5.677  43.501   1185
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.25), residues: 1069
  helix:  0.62 (0.24), residues: 483
  sheet: -1.27 (0.43), residues: 138
  loop : -1.11 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 244 
 TYR   0.015   0.002   TYR C  46 
 PHE   0.016   0.002   PHE C 671 
 TRP   0.014   0.002   TRP J  81 
 HIS   0.006   0.001   HIS J  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00435 /  0.20 ( 8845)
  covalent geometry    : angle       0.68017 /  0.35 (11943)
  hydrogen bonds       : bond        0.03960 /  2.65 (  409)
  hydrogen bonds       : angle       5.54903 /  3.88 ( 1131)
  Misc. bond           : bond        0.00246 /  0.13 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   46 MET cc_start: 0.6874 (ptp) cc_final: 0.6531 (ptp)
REVERT: J  178 MET cc_start: 0.7308 (tmm) cc_final: 0.6932 (tmm)
REVERT: J  192 MET cc_start: 0.8924 (ttm) cc_final: 0.8631 (tpp)
REVERT: J  242 TYR cc_start: 0.8010 (t80) cc_final: 0.7464 (t80)
REVERT: J  271 MET cc_start: 0.6981 (tpt) cc_final: 0.6508 (tpt)
REVERT: J  305 THR cc_start: 0.8744 (m) cc_final: 0.8520 (m)
REVERT: J  307 MET cc_start: 0.8077 (mmp) cc_final: 0.7622 (mmm)
REVERT: J  327 MET cc_start: 0.8014 (ptm) cc_final: 0.7585 (pmm)
REVERT: C    6 MET cc_start: 0.8712 (mtp) cc_final: 0.8501 (mtp)
REVERT: C   77 MET cc_start: 0.7999 (mpp) cc_final: 0.7749 (mpp)
REVERT: C  113 MET cc_start: 0.7707 (mtp) cc_final: 0.7150 (mtt)
REVERT: C  358 MET cc_start: 0.8613 (mmt) cc_final: 0.8217 (mmm)
REVERT: C  369 GLN cc_start: 0.7464 (tm-30) cc_final: 0.7087 (tm-30)
REVERT: C  389 MET cc_start: 0.8492 (mpp) cc_final: 0.8282 (mpp)
REVERT: C  486 LEU cc_start: 0.9252 (mt) cc_final: 0.8798 (tt)
REVERT: C  517 ASP cc_start: 0.9029 (m-30) cc_final: 0.8698 (t0)
REVERT: C  581 VAL cc_start: 0.8801 (t) cc_final: 0.8355 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0735
  time to fit residues: 11.2183
Evaluate side-chains
  78 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 34 optimal weight:    0.6980
   chunk 103 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 653 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.045079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.037296 restraints weight = 75958.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.038450 restraints weight = 50464.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.039303 restraints weight = 36658.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.039958 restraints weight = 28277.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.040469 restraints weight = 22836.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7554
moved from start:          0.4331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8846  Z= 0.122
  Angle     :  0.608   8.421  11943  Z= 0.311
  Chirality :  0.043   0.237   1302
  Planarity :  0.004   0.055   1537
  Dihedral  :  5.460  44.161   1185
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.26), residues: 1069
  helix:  0.84 (0.24), residues: 489
  sheet: -1.01 (0.45), residues: 138
  loop : -0.85 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 244 
 TYR   0.012   0.001   TYR C 288 
 PHE   0.013   0.001   PHE C 671 
 TRP   0.012   0.001   TRP J  81 
 HIS   0.004   0.001   HIS C 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00268 /  0.12 ( 8845)
  covalent geometry    : angle       0.60772 /  0.31 (11943)
  hydrogen bonds       : bond        0.03419 /  2.25 (  409)
  hydrogen bonds       : angle       5.28542 /  3.68 ( 1131)
  Misc. bond           : bond        0.00236 /  0.12 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   46 MET cc_start: 0.6948 (ptp) cc_final: 0.6645 (ptp)
REVERT: J  178 MET cc_start: 0.7393 (tmm) cc_final: 0.7046 (tmm)
REVERT: J  271 MET cc_start: 0.6863 (tpt) cc_final: 0.6455 (tpt)
REVERT: J  307 MET cc_start: 0.8030 (mmp) cc_final: 0.7567 (mmm)
REVERT: C    6 MET cc_start: 0.8707 (mtp) cc_final: 0.8241 (ttm)
REVERT: C   29 ARG cc_start: 0.8183 (mmm160) cc_final: 0.7871 (mmm160)
REVERT: C  113 MET cc_start: 0.7737 (mtp) cc_final: 0.7168 (mtt)
REVERT: C  486 LEU cc_start: 0.9195 (mt) cc_final: 0.8748 (tt)
REVERT: C  517 ASP cc_start: 0.8993 (m-30) cc_final: 0.8730 (t0)
REVERT: C  575 GLU cc_start: 0.8877 (pt0) cc_final: 0.8407 (pp20)
REVERT: C  581 VAL cc_start: 0.8887 (t) cc_final: 0.8489 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0745
  time to fit residues: 11.7038
Evaluate side-chains
  78 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 50 optimal weight:    0.4980
   chunk 11 optimal weight:    4.9990
   chunk 88 optimal weight:    0.0870
   chunk 33 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    0.8560

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
J  75 HIS
** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 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 = 0.3075 r_free = 0.3075 target = 0.044785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.037060 restraints weight = 76971.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.038211 restraints weight = 51047.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.039081 restraints weight = 37008.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.039742 restraints weight = 28435.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.040252 restraints weight = 22959.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.4542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8846  Z= 0.131
  Angle     :  0.628   8.137  11943  Z= 0.322
  Chirality :  0.043   0.234   1302
  Planarity :  0.004   0.047   1537
  Dihedral  :  5.428  42.834   1185
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.27), residues: 1069
  helix:  0.91 (0.24), residues: 488
  sheet: -0.72 (0.46), residues: 138
  loop : -0.78 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 654 
 TYR   0.016   0.001   TYR J 242 
 PHE   0.014   0.001   PHE C 671 
 TRP   0.012   0.001   TRP J  81 
 HIS   0.014   0.001   HIS J  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 8845)
  covalent geometry    : angle       0.62780 /  0.32 (11943)
  hydrogen bonds       : bond        0.03495 /  2.27 (  409)
  hydrogen bonds       : angle       5.37681 /  3.72 ( 1131)
  Misc. bond           : bond        0.00206 /  0.11 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   46 MET cc_start: 0.7263 (ptp) cc_final: 0.7045 (ptp)
REVERT: J  134 MET cc_start: 0.8156 (tmm) cc_final: 0.7853 (tmm)
REVERT: J  192 MET cc_start: 0.9049 (tpp) cc_final: 0.8643 (tpp)
REVERT: J  242 TYR cc_start: 0.8564 (t80) cc_final: 0.8318 (t80)
REVERT: J  271 MET cc_start: 0.6729 (tpt) cc_final: 0.6355 (tpt)
REVERT: J  305 THR cc_start: 0.8844 (m) cc_final: 0.8598 (m)
REVERT: J  307 MET cc_start: 0.8096 (mmp) cc_final: 0.7618 (mmm)
REVERT: C    6 MET cc_start: 0.8711 (mtp) cc_final: 0.8233 (ttm)
REVERT: C   29 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7873 (mmm160)
REVERT: C  113 MET cc_start: 0.7744 (mtp) cc_final: 0.7137 (mtt)
REVERT: C  358 MET cc_start: 0.8760 (mmt) cc_final: 0.8344 (mmm)
REVERT: C  486 LEU cc_start: 0.9214 (mt) cc_final: 0.8758 (tt)
REVERT: C  517 ASP cc_start: 0.9022 (m-30) cc_final: 0.8753 (t0)
REVERT: C  540 MET cc_start: 0.7534 (mmp) cc_final: 0.6770 (mtm)
REVERT: C  575 GLU cc_start: 0.8893 (pt0) cc_final: 0.8425 (pp20)
REVERT: C  581 VAL cc_start: 0.8847 (t) cc_final: 0.8386 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0760
  time to fit residues: 11.0636
Evaluate side-chains
  76 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 49 optimal weight:    0.2980
   chunk 54 optimal weight:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 106 optimal weight:    0.0040
   chunk 17 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    0.5796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 223 GLN
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 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 = 0.3093 r_free = 0.3093 target = 0.045291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.037664 restraints weight = 77123.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.038779 restraints weight = 51863.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.039618 restraints weight = 37947.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.040263 restraints weight = 29411.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.040776 restraints weight = 23828.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.4708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8846  Z= 0.113
  Angle     :  0.631  10.160  11943  Z= 0.316
  Chirality :  0.043   0.231   1302
  Planarity :  0.004   0.048   1537
  Dihedral  :  5.431  47.121   1185
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.27), residues: 1069
  helix:  0.99 (0.24), residues: 490
  sheet: -0.64 (0.46), residues: 142
  loop : -0.61 (0.32), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 244 
 TYR   0.022   0.001   TYR C 103 
 PHE   0.013   0.001   PHE C 490 
 TRP   0.010   0.001   TRP J  81 
 HIS   0.004   0.001   HIS C 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.11 ( 8845)
  covalent geometry    : angle       0.63112 /  0.32 (11943)
  hydrogen bonds       : bond        0.03294 /  2.16 (  409)
  hydrogen bonds       : angle       5.24285 /  3.61 ( 1131)
  Misc. bond           : bond        0.00542 /  0.29 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  178 MET cc_start: 0.7359 (tmm) cc_final: 0.7100 (tmm)
REVERT: J  192 MET cc_start: 0.9002 (tpp) cc_final: 0.8605 (tpt)
REVERT: J  242 TYR cc_start: 0.8042 (t80) cc_final: 0.7581 (t80)
REVERT: J  271 MET cc_start: 0.6513 (tpt) cc_final: 0.6221 (tpt)
REVERT: J  294 ASP cc_start: 0.9405 (m-30) cc_final: 0.8937 (p0)
REVERT: J  305 THR cc_start: 0.8893 (m) cc_final: 0.8630 (m)
REVERT: J  307 MET cc_start: 0.8118 (mmp) cc_final: 0.7658 (mmm)
REVERT: C    6 MET cc_start: 0.8704 (mtp) cc_final: 0.8227 (ttm)
REVERT: C   29 ARG cc_start: 0.8176 (mmm160) cc_final: 0.7888 (mmm160)
REVERT: C  113 MET cc_start: 0.7766 (mtp) cc_final: 0.7147 (mtt)
REVERT: C  165 MET cc_start: 0.7341 (tpp) cc_final: 0.7019 (tpt)
REVERT: C  389 MET cc_start: 0.8560 (mpp) cc_final: 0.8125 (mpp)
REVERT: C  486 LEU cc_start: 0.9186 (mt) cc_final: 0.8708 (tt)
REVERT: C  517 ASP cc_start: 0.9005 (m-30) cc_final: 0.8682 (t0)
REVERT: C  540 MET cc_start: 0.7543 (mmp) cc_final: 0.6589 (mtm)
REVERT: C  575 GLU cc_start: 0.8895 (pt0) cc_final: 0.8374 (pp20)
REVERT: C  581 VAL cc_start: 0.8829 (t) cc_final: 0.8472 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.0806
  time to fit residues: 12.1315
Evaluate side-chains
  73 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 81 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 68 optimal weight:    0.4980
   chunk 66 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0870
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.7162

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 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 = 0.3090 r_free = 0.3090 target = 0.045366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.037850 restraints weight = 77675.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.038968 restraints weight = 51899.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.039808 restraints weight = 37883.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.040443 restraints weight = 29244.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.040946 restraints weight = 23712.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.4831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8846  Z= 0.120
  Angle     :  0.634   8.231  11943  Z= 0.319
  Chirality :  0.043   0.229   1302
  Planarity :  0.004   0.047   1537
  Dihedral  :  5.359  46.974   1185
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.27), residues: 1069
  helix:  1.06 (0.24), residues: 490
  sheet: -0.53 (0.47), residues: 140
  loop : -0.53 (0.32), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 654 
 TYR   0.013   0.001   TYR C 103 
 PHE   0.011   0.001   PHE C 490 
 TRP   0.010   0.001   TRP J  81 
 HIS   0.005   0.001   HIS C  97 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 ( 8845)
  covalent geometry    : angle       0.63353 /  0.32 (11943)
  hydrogen bonds       : bond        0.03305 /  2.19 (  409)
  hydrogen bonds       : angle       5.24245 /  3.63 ( 1131)
  Misc. bond           : bond        0.00404 /  0.21 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J  192 MET cc_start: 0.8983 (tpp) cc_final: 0.8494 (tpp)
REVERT: J  242 TYR cc_start: 0.8027 (t80) cc_final: 0.7535 (t80)
REVERT: J  271 MET cc_start: 0.6621 (tpt) cc_final: 0.6314 (tpt)
REVERT: J  305 THR cc_start: 0.8852 (m) cc_final: 0.8585 (m)
REVERT: J  307 MET cc_start: 0.8132 (mmp) cc_final: 0.7672 (mmm)
REVERT: C    6 MET cc_start: 0.8704 (mtp) cc_final: 0.8229 (ttm)
REVERT: C   29 ARG cc_start: 0.8201 (mmm160) cc_final: 0.7922 (mmm160)
REVERT: C  113 MET cc_start: 0.7739 (mtp) cc_final: 0.7131 (mtt)
REVERT: C  358 MET cc_start: 0.8610 (mmt) cc_final: 0.8286 (mmm)
REVERT: C  389 MET cc_start: 0.8543 (mpp) cc_final: 0.8124 (mpp)
REVERT: C  486 LEU cc_start: 0.9216 (mt) cc_final: 0.8739 (tt)
REVERT: C  517 ASP cc_start: 0.8978 (m-30) cc_final: 0.8659 (t0)
REVERT: C  540 MET cc_start: 0.7562 (mmp) cc_final: 0.6662 (mtm)
REVERT: C  575 GLU cc_start: 0.8862 (pt0) cc_final: 0.8519 (pp20)
REVERT: C  581 VAL cc_start: 0.8815 (t) cc_final: 0.8435 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0689
  time to fit residues: 10.3256
Evaluate side-chains
  73 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 52 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3054 r_free = 0.3054 target = 0.044486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.037211 restraints weight = 79729.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.038314 restraints weight = 53539.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.039132 restraints weight = 39014.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.039746 restraints weight = 30160.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.040241 restraints weight = 24384.345|
|-----------------------------------------------------------------------------|
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.5016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8846  Z= 0.178
  Angle     :  0.696   8.316  11943  Z= 0.354
  Chirality :  0.044   0.228   1302
  Planarity :  0.004   0.047   1537
  Dihedral  :  5.685  48.944   1185
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.27), residues: 1069
  helix:  0.92 (0.24), residues: 489
  sheet: -0.69 (0.44), residues: 149
  loop : -0.58 (0.32), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 244 
 TYR   0.016   0.001   TYR C 103 
 PHE   0.010   0.001   PHE C 541 
 TRP   0.014   0.002   TRP J 358 
 HIS   0.004   0.001   HIS C 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.18 ( 8845)
  covalent geometry    : angle       0.69648 /  0.35 (11943)
  hydrogen bonds       : bond        0.03788 /  2.54 (  409)
  hydrogen bonds       : angle       5.54399 /  3.86 ( 1131)
  Misc. bond           : bond        0.00403 /  0.21 (    1)

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
REVERT: J  192 MET cc_start: 0.8947 (tpp) cc_final: 0.8484 (tpp)
REVERT: J  242 TYR cc_start: 0.8089 (t80) cc_final: 0.7591 (t80)
REVERT: J  271 MET cc_start: 0.6774 (tpt) cc_final: 0.6404 (tpt)
REVERT: J  305 THR cc_start: 0.8776 (m) cc_final: 0.8496 (m)
REVERT: J  307 MET cc_start: 0.8203 (mmp) cc_final: 0.7705 (mmm)
REVERT: C    6 MET cc_start: 0.8803 (mtp) cc_final: 0.8575 (mtm)
REVERT: C   29 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7927 (mmm160)
REVERT: C  113 MET cc_start: 0.7689 (mtp) cc_final: 0.7156 (mtt)
REVERT: C  358 MET cc_start: 0.8562 (mmt) cc_final: 0.8287 (mmm)
REVERT: C  389 MET cc_start: 0.8555 (mpp) cc_final: 0.8151 (mpp)
REVERT: C  486 LEU cc_start: 0.9233 (mt) cc_final: 0.8776 (tt)
REVERT: C  517 ASP cc_start: 0.8956 (m-30) cc_final: 0.8673 (t0)
REVERT: C  575 GLU cc_start: 0.8867 (pt0) cc_final: 0.8483 (pp20)
REVERT: C  581 VAL cc_start: 0.8728 (t) cc_final: 0.8289 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0688
  time to fit residues: 10.2286
Evaluate side-chains
  74 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 50 optimal weight:    0.2980
   chunk 106 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 762 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.045064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.037575 restraints weight = 77659.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.038733 restraints weight = 51352.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2900 r_free = 0.2900 target = 0.039594 restraints weight = 37060.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2922 r_free = 0.2922 target = 0.040241 restraints weight = 28418.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.040749 restraints weight = 22798.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.2937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.5150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8846  Z= 0.119
  Angle     :  0.639   8.829  11943  Z= 0.320
  Chirality :  0.043   0.227   1302
  Planarity :  0.004   0.047   1537
  Dihedral  :  5.449  48.258   1185
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.27), residues: 1069
  helix:  1.11 (0.24), residues: 490
  sheet: -0.59 (0.48), residues: 131
  loop : -0.54 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 654 
 TYR   0.015   0.001   TYR C 103 
 PHE   0.011   0.001   PHE C 490 
 TRP   0.012   0.001   TRP J  81 
 HIS   0.004   0.001   HIS C 359 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 ( 8845)
  covalent geometry    : angle       0.63867 /  0.32 (11943)
  hydrogen bonds       : bond        0.03400 /  2.26 (  409)
  hydrogen bonds       : angle       5.29228 /  3.67 ( 1131)
  Misc. bond           : bond        0.00317 /  0.17 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1361.16 seconds
wall clock time: 24 minutes 24.78 seconds (1464.78 seconds total)