Starting phenix.real_space_refine
on Thu Feb  5 00:10:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ea3_47825/02_2026/9ea3_47825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ea3_47825/02_2026/9ea3_47825.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ea3_47825/02_2026/9ea3_47825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ea3_47825/02_2026/9ea3_47825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ea3_47825/02_2026/9ea3_47825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ea3_47825/02_2026/9ea3_47825.cif"
  }
  resolution = 3.99
  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=   0.001 sd=   0.012
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      56      5.49       5
     S      67      5.16       5
     C    8547      2.51       5
     N    2289      2.21       5
     O    2720      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13679
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 898, 7284
          Classifications: {'peptide': 898}
          Link IDs: {'PTRANS': 40, 'TRANS': 857}
    Chain: "B"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1749
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 7, 'TRANS': 220}
    Chain: "D"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1749
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 7, 'TRANS': 220}
    Chain: "E"
      Number of atoms: 1749
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1749
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 7, 'TRANS': 220}
    Chain: "P"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 512
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "T"
      Number of atoms: 636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 636
          Classifications: {'DNA': 31}
          Link IDs: {'rna3p': 30}
  Time building chain proxies: 3.86, per 1000 atoms: 0.28
  Number of scatterers: 13679
  At special positions: 0
  Unit cell: (105.156, 105.984, 136.62, 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      67     16.00
     P      56     15.00
     O    2720      8.00
     N    2289      7.00
     C    8547      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 517.1 milliseconds
  

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2964

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 18 sheets defined
      36.9% alpha, 22.9% beta
      25 base pairs and 40 stacking pairs defined.
    Time for finding SS restraints: 2.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 76
      removed outlier: 3.516A  pdb=" N   ILE A  76 " --> pdb=" O   ARG A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 96
      removed outlier: 3.550A  pdb=" N   TYR A  95 " --> pdb=" O   ILE A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 106
      removed outlier: 3.805A  pdb=" N   VAL A 106 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 166
    Processing helix  chain 'A' and resid 167 through 171
    Processing helix  chain 'A' and resid 176 through 181
      removed outlier: 3.591A  pdb=" N   LEU A 180 " --> pdb=" O   PRO A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 205
    Processing helix  chain 'A' and resid 218 through 232
    Processing helix  chain 'A' and resid 233 through 240
      removed outlier: 3.513A  pdb=" N   PHE A 239 " --> pdb=" O   SER A 235 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER A 240 " --> pdb=" O   MET A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 278
      removed outlier: 3.619A  pdb=" N   ALA A 278 " --> pdb=" O   TYR A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 296
    Processing helix  chain 'A' and resid 305 through 313
      removed outlier: 3.899A  pdb=" N   ARG A 310 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   GLU A 311 " --> pdb=" O   ASN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 336
    Processing helix  chain 'A' and resid 337 through 349
    Processing helix  chain 'A' and resid 351 through 356
    Processing helix  chain 'A' and resid 357 through 373
    Processing helix  chain 'A' and resid 411 through 421
    Processing helix  chain 'A' and resid 435 through 441
      removed outlier: 3.623A  pdb=" N   TYR A 439 " --> pdb=" O   PRO A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 503
    Processing helix  chain 'A' and resid 520 through 528
    Processing helix  chain 'A' and resid 531 through 568
      removed outlier: 4.246A  pdb=" N   TYR A 564 " --> pdb=" O   ILE A 560 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   GLY A 565 " --> pdb=" O   ASN A 561 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLY A 568 " --> pdb=" O   TYR A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 607
    Processing helix  chain 'A' and resid 626 through 634
      removed outlier: 3.521A  pdb=" N   ILE A 630 " --> pdb=" O   VAL A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 655
    Processing helix  chain 'A' and resid 656 through 671
    Processing helix  chain 'A' and resid 735 through 752
    Processing helix  chain 'A' and resid 753 through 769
      removed outlier: 3.560A  pdb=" N   VAL A 757 " --> pdb=" O   GLY A 753 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ARG A 769 " --> pdb=" O   GLU A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 771
      No H-bonds generated for 'chain 'A' and resid 770 through 771'
    Processing helix  chain 'A' and resid 772 through 776
      removed outlier: 3.763A  pdb=" N   ILE A 776 " --> pdb=" O   TYR A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 784 through 787
    Processing helix  chain 'A' and resid 799 through 813
    Processing helix  chain 'A' and resid 851 through 861
      removed outlier: 3.952A  pdb=" N   SER A 856 " --> pdb=" O   LYS A 852 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   ASP A 857 " --> pdb=" O   GLU A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 863 through 872
      removed outlier: 3.637A  pdb=" N   LEU A 867 " --> pdb=" O   ASP A 863 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 872 through 883
    Processing helix  chain 'A' and resid 892 through 896
      removed outlier: 4.425A  pdb=" N   PHE A 895 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 16
      removed outlier: 3.583A  pdb=" N   THR B  16 " --> pdb=" O   LYS B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 67
      removed outlier: 3.685A  pdb=" N   VAL B  67 " --> pdb=" O   ILE B  63 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 133
    Processing helix  chain 'B' and resid 185 through 187
      No H-bonds generated for 'chain 'B' and resid 185 through 187'
    Processing helix  chain 'D' and resid 4 through 18
    Processing helix  chain 'D' and resid 56 through 67
      removed outlier: 3.513A  pdb=" N   PHE D  60 " --> pdb=" O   ASP D  56 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 131
      removed outlier: 4.353A  pdb=" N   ARG D 131 " --> pdb=" O   LEU D 127 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 185 through 187
      No H-bonds generated for 'chain 'D' and resid 185 through 187'
    Processing helix  chain 'E' and resid 4 through 16
      removed outlier: 3.501A  pdb=" N   THR E  16 " --> pdb=" O   LYS E  12 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 56 through 67
    Processing helix  chain 'E' and resid 119 through 134
    Processing helix  chain 'E' and resid 185 through 187
      No H-bonds generated for 'chain 'E' and resid 185 through 187'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11
      removed outlier: 6.157A  pdb=" N   TYR A   5 " --> pdb=" O   ILE A  20 " (cutoff:3.500A)
      removed outlier: 5.958A  pdb=" N   ILE A  20 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59
      removed outlier: 3.733A  pdb=" N   PHE A  38 " --> pdb=" O   LEU A  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 183 through 185
      removed outlier: 5.451A  pdb=" N   ALA A 109 " --> pdb=" O   THR A 211 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE A 210 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151
    Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 247
    Processing sheet with id=AA6, first strand: chain 'A' and resid 614 through 618
      removed outlier: 5.415A  pdb=" N   ILE A 614 " --> pdb=" O   CYS A 625 " (cutoff:3.500A)
      removed outlier: 5.706A  pdb=" N   CYS A 625 " --> pdb=" O   ILE A 614 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   ILE A 404 " --> pdb=" O   ILE A 685 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   ILE A 685 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   SER A 406 " --> pdb=" O   GLU A 683 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   GLU A 683 " --> pdb=" O   MET A 712 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   MET A 712 " --> pdb=" O   GLU A 683 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ILE A 685 " --> pdb=" O   TYR A 710 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ARG A 704 " --> pdb=" O   LYS A 700 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 614 through 618
      removed outlier: 5.415A  pdb=" N   ILE A 614 " --> pdb=" O   CYS A 625 " (cutoff:3.500A)
      removed outlier: 5.706A  pdb=" N   CYS A 625 " --> pdb=" O   ILE A 614 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   ILE A 404 " --> pdb=" O   ILE A 685 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   ILE A 685 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   SER A 406 " --> pdb=" O   GLU A 683 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   GLU A 683 " --> pdb=" O   MET A 712 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   MET A 712 " --> pdb=" O   GLU A 683 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   ILE A 685 " --> pdb=" O   TYR A 710 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   LEU A 707 " --> pdb=" O   LYS A 723 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   ASP A 711 " --> pdb=" O   GLU A 719 " (cutoff:3.500A)
      removed outlier: 11.525A  pdb=" N   GLU A 719 " --> pdb=" O   ASP A 711 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 427 through 430
    Processing sheet with id=AA9, first strand: chain 'A' and resid 789 through 790
      removed outlier: 3.695A  pdb=" N   ASP A 790 " --> pdb=" O   TRP A 793 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 826 through 830
    Processing sheet with id=AB2, first strand: chain 'B' and resid 21 through 23
    Processing sheet with id=AB3, first strand: chain 'B' and resid 26 through 32
      removed outlier: 5.527A  pdb=" N   GLN B  27 " --> pdb=" O   ILE B  44 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 72 through 75
      removed outlier: 6.622A  pdb=" N   ILE E 147 " --> pdb=" O   LEU E 169 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   VAL E 142 " --> pdb=" O   PHE E 178 " (cutoff:3.500A)
      removed outlier: 6.296A  pdb=" N   PHE E 178 " --> pdb=" O   VAL E 142 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 225 through 227
      removed outlier: 6.250A  pdb=" N   PHE B 178 " --> pdb=" O   VAL B 142 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   VAL B 142 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ILE B 147 " --> pdb=" O   LEU B 169 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   TYR B 165 " --> pdb=" O   GLY B 151 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 21 through 23
    Processing sheet with id=AB7, first strand: chain 'D' and resid 26 through 32
      removed outlier: 5.964A  pdb=" N   PHE D  28 " --> pdb=" O   ASP D  46 " (cutoff:3.500A)
      removed outlier: 10.338A  pdb=" N   ASP D  46 " --> pdb=" O   PHE D  28 " (cutoff:3.500A)
      removed outlier: 10.978A  pdb=" N   MET D  30 " --> pdb=" O   ILE D  44 " (cutoff:3.500A)
      removed outlier: 11.275A  pdb=" N   ILE D  44 " --> pdb=" O   MET D  30 " (cutoff:3.500A)
      removed outlier: 11.553A  pdb=" N   ARG D  32 " --> pdb=" O   ALA D  42 " (cutoff:3.500A)
      removed outlier: 11.958A  pdb=" N   ALA D  42 " --> pdb=" O   ARG D  32 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 225 through 227
      removed outlier: 6.535A  pdb=" N   PHE D 178 " --> pdb=" O   VAL D 142 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL D 142 " --> pdb=" O   PHE D 178 " (cutoff:3.500A)
      removed outlier: 6.939A  pdb=" N   ILE D 147 " --> pdb=" O   LEU D 169 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   TYR D 165 " --> pdb=" O   GLY D 151 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 26 through 32
      removed outlier: 5.155A  pdb=" N   GLN E  27 " --> pdb=" O   ILE E  44 " (cutoff:3.500A)

    633 hydrogen bonds defined for protein.
    1743 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      60 hydrogen bonds
      120 hydrogen bond angles
      0 basepair planarities
      25 basepair parallelities
      40 stacking parallelities
  Total time for adding SS restraints: 3.03

  Time building geometry restraints manager: 1.94 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3715
        1.33 -     1.45: 2633
        1.45 -     1.57: 7496
        1.57 -     1.69: 110
        1.69 -     1.81: 120
  Bond restraints: 14074
  Sorted by residual:
  bond pdb=" N   ILE D 182 "
       pdb=" CA  ILE D 182 "
    ideal  model  delta    sigma   weight residual
    1.458  1.496 -0.038 1.19e-02 7.06e+03 1.01e+01
  bond pdb=" N   ILE A 724 "
       pdb=" CA  ILE A 724 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.22e-02 6.72e+03 8.75e+00
  bond pdb=" N   GLY A 429 "
       pdb=" CA  GLY A 429 "
    ideal  model  delta    sigma   weight residual
    1.447  1.477 -0.030 1.03e-02 9.43e+03 8.54e+00
  bond pdb=" N   ILE A 427 "
       pdb=" CA  ILE A 427 "
    ideal  model  delta    sigma   weight residual
    1.458  1.494 -0.037 1.27e-02 6.20e+03 8.41e+00
  bond pdb=" N   ILE D 181 "
       pdb=" CA  ILE D 181 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.20e-02 6.94e+03 8.26e+00
  ... (remaining 14069 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 18436
        1.54 -     3.07: 687
        3.07 -     4.61: 87
        4.61 -     6.15: 31
        6.15 -     7.68: 12
  Bond angle restraints: 19253
  Sorted by residual:
  angle pdb=" CA  GLY D 192 "
        pdb=" C   GLY D 192 "
        pdb=" O   GLY D 192 "
      ideal   model   delta    sigma   weight residual
     121.96  118.16    3.80 1.02e+00 9.61e-01 1.39e+01
  angle pdb=" N   GLU A  74 "
        pdb=" CA  GLU A  74 "
        pdb=" C   GLU A  74 "
      ideal   model   delta    sigma   weight residual
     112.89  108.50    4.39 1.24e+00 6.50e-01 1.26e+01
  angle pdb=" O3'  DA T  24 "
        pdb=" P    DT T  25 "
        pdb=" O5'  DT T  25 "
      ideal   model   delta    sigma   weight residual
     104.00   98.73    5.27 1.50e+00 4.44e-01 1.23e+01
  angle pdb=" CA  ASP A 269 "
        pdb=" C   ASP A 269 "
        pdb=" O   ASP A 269 "
      ideal   model   delta    sigma   weight residual
     121.99  118.13    3.86 1.14e+00 7.69e-01 1.15e+01
  angle pdb=" N   GLU A 216 "
        pdb=" CA  GLU A 216 "
        pdb=" C   GLU A 216 "
      ideal   model   delta    sigma   weight residual
     113.01  109.02    3.99 1.20e+00 6.94e-01 1.11e+01
  ... (remaining 19248 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.19: 7548
       22.19 -    44.39: 613
       44.39 -    66.58: 201
       66.58 -    88.77: 7
       88.77 -   110.97: 1
  Dihedral angle restraints: 8370
    sinusoidal: 3763
      harmonic: 4607
  Sorted by residual:
  dihedral pdb=" CA  PRO A 455 "
           pdb=" C   PRO A 455 "
           pdb=" N   ASN A 456 "
           pdb=" CA  ASN A 456 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.14   17.86     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  PRO A 851 "
           pdb=" C   PRO A 851 "
           pdb=" N   LYS A 852 "
           pdb=" CA  LYS A 852 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.00  -17.00     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" CA  ILE D  21 "
           pdb=" C   ILE D  21 "
           pdb=" N   MET D  22 "
           pdb=" CA  MET D  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.61   16.39     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 8367 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.115: 2055
       0.115 -    0.229: 52
       0.229 -    0.344: 0
       0.344 -    0.459: 0
       0.459 -    0.573: 13
  Chirality restraints: 2120
  Sorted by residual:
  chirality pdb=" P    DG P  24 "
            pdb=" OP1  DG P  24 "
            pdb=" OP2  DG P  24 "
            pdb=" O5'  DG P  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.92   -0.57 2.00e-01 2.50e+01 8.22e+00
  chirality pdb=" P    DT P  22 "
            pdb=" OP1  DT P  22 "
            pdb=" OP2  DT P  22 "
            pdb=" O5'  DT P  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.88   -0.54 2.00e-01 2.50e+01 7.25e+00
  chirality pdb=" P    DA P  21 "
            pdb=" OP1  DA P  21 "
            pdb=" OP2  DA P  21 "
            pdb=" O5'  DA P  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.88   -0.54 2.00e-01 2.50e+01 7.21e+00
  ... (remaining 2117 not shown)

  Planarity restraints: 2287
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 468 "   -0.027 5.00e-02 4.00e+02   4.15e-02 2.75e+00
        pdb=" N   PRO A 469 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 469 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 469 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG T  30 "    0.019 2.00e-02 2.50e+03   8.40e-03 2.12e+00
        pdb=" N9   DG T  30 "   -0.021 2.00e-02 2.50e+03
        pdb=" C8   DG T  30 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7   DG T  30 "    0.000 2.00e-02 2.50e+03
        pdb=" C5   DG T  30 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DG T  30 "    0.003 2.00e-02 2.50e+03
        pdb=" O6   DG T  30 "    0.003 2.00e-02 2.50e+03
        pdb=" N1   DG T  30 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DG T  30 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2   DG T  30 "    0.000 2.00e-02 2.50e+03
        pdb=" N3   DG T  30 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DG T  30 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E  96 "   -0.022 5.00e-02 4.00e+02   3.34e-02 1.78e+00
        pdb=" N   PRO E  97 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO E  97 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO E  97 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 2284 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1260
        2.74 -     3.28: 14952
        3.28 -     3.82: 24959
        3.82 -     4.36: 28538
        4.36 -     4.90: 45567
  Nonbonded interactions: 115276
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 845 "
            pdb=" OG1 THR A 848 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG  SER A 345 "
            pdb=" O   MET A 350 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   ASN D  13 "
            pdb=" OG1 THR D  16 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   ASP A 160 "
            pdb=" NE2 GLN A 315 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" O   LYS D   5 "
            pdb=" OG1 THR D   8 "
     model   vdw
     2.220 3.040
  ... (remaining 115271 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'E'
}

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:             2.300
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     17.410
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
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      :  0.005   0.047  14074  Z= 0.286
  Angle     :  0.690   7.681  19253  Z= 0.411
  Chirality :  0.061   0.573   2120
  Planarity :  0.004   0.041   2287
  Dihedral  : 16.765 110.966   5406
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 19.23
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.07 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 11.26 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.21), residues: 1574
  helix:  0.97 (0.23), residues: 533
  sheet: -0.52 (0.26), residues: 348
  loop : -0.83 (0.24), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  27 
 TYR   0.018   0.001   TYR B  39 
 PHE   0.012   0.001   PHE A 698 
 TRP   0.010   0.001   TRP A 593 
 HIS   0.005   0.001   HIS D 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 (14074)
  covalent geometry    : angle       0.69043 (19253)
  hydrogen bonds       : bond        0.13171 (  681)
  hydrogen bonds       : angle       6.54558 ( 1863)

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

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

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 220
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.4425 (ptt) cc_final: 0.3286 (ppp)
REVERT: A   83 MET cc_start: 0.6722 (tpp) cc_final: 0.6518 (tpp)
REVERT: A   85 ASP cc_start: 0.8869 (t0) cc_final: 0.8579 (t0)
REVERT: A  238 ARG cc_start: 0.8807 (mtp-110) cc_final: 0.8394 (ptm160)
REVERT: A  486 MET cc_start: 0.8083 (ttp) cc_final: 0.7727 (tpt)
REVERT: A  667 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8757 (mp)
REVERT: A  671 MET cc_start: 0.8583 (tpp) cc_final: 0.8335 (tpp)
REVERT: A  721 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.7136 (p-80)
REVERT: A  881 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8660 (pp20)
REVERT: B   14 PHE cc_start: 0.8800 (m-10) cc_final: 0.8509 (m-80)
REVERT: B   32 ARG cc_start: 0.8244 (tpp-160) cc_final: 0.8029 (tpp-160)
REVERT: B  128 ARG cc_start: 0.9208 (mmt90) cc_final: 0.8939 (mmm-85)
REVERT: B  215 ASN cc_start: 0.8001 (m-40) cc_final: 0.7724 (m-40)
REVERT: D   30 MET cc_start: 0.8102 (ptm) cc_final: 0.7510 (ptp)
REVERT: D   55 TYR cc_start: 0.8120 (t80) cc_final: 0.7864 (t80)
REVERT: D   58 ASN cc_start: 0.8656 (OUTLIER) cc_final: 0.8411 (m-40)
REVERT: D   70 ASP cc_start: 0.7597 (t70) cc_final: 0.7332 (t70)
REVERT: D  128 ARG cc_start: 0.8265 (tpp80) cc_final: 0.7892 (ttm170)
REVERT: D  198 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9048 (mp)
REVERT: E    1 MET cc_start: 0.7607 (mmt) cc_final: 0.7189 (mmt)
REVERT: E  125 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8763 (tm-30)
REVERT: E  180 PHE cc_start: 0.8338 (m-10) cc_final: 0.7446 (m-10)
REVERT: E  187 MET cc_start: 0.9181 (mmm) cc_final: 0.8936 (mmm)
  outliers start: 63
  outliers final: 32
  residues processed: 270
  average time/residue: 0.1279
  time to fit residues: 50.5178
Evaluate side-chains
  204 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 167
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  622 VAL
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  721 HIS
Chi-restraints excluded: chain A residue  729 THR
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain D residue   58 ASN
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  189 MET
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain E residue    6 ASP
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  195 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 98 optimal weight:    0.0670
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    0.1980
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:   20.0000
   chunk 77 optimal weight:    0.3980
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    6.9990
   overall best weight:    0.7320

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
D  13 ASN
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 176 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.109051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.083402 restraints weight = 48184.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.085440 restraints weight = 29367.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.086189 restraints weight = 19629.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.086500 restraints weight = 18434.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.086857 restraints weight = 16562.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14074  Z= 0.136
  Angle     :  0.621  10.656  19253  Z= 0.328
  Chirality :  0.045   0.308   2120
  Planarity :  0.004   0.050   2287
  Dihedral  : 18.206 156.695   2399
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 15.23 %
    Favored  : 80.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.15 (0.21), residues: 1574
  helix:  0.88 (0.22), residues: 548
  sheet: -0.33 (0.26), residues: 369
  loop : -0.69 (0.25), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 226 
 TYR   0.020   0.001   TYR B  39 
 PHE   0.017   0.001   PHE B 109 
 TRP   0.014   0.001   TRP B  92 
 HIS   0.004   0.001   HIS B 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (14074)
  covalent geometry    : angle       0.62141 (19253)
  hydrogen bonds       : bond        0.04124 (  681)
  hydrogen bonds       : angle       5.45541 ( 1863)

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

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

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 206
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    5 TYR cc_start: 0.7484 (p90) cc_final: 0.7206 (p90)
REVERT: A   30 GLU cc_start: 0.7793 (pp20) cc_final: 0.7489 (pp20)
REVERT: A   37 MET cc_start: 0.4401 (ptt) cc_final: 0.3240 (ppp)
REVERT: A   85 ASP cc_start: 0.8568 (t0) cc_final: 0.8147 (t0)
REVERT: A  236 MET cc_start: 0.7638 (mtp) cc_final: 0.7079 (mpp)
REVERT: A  238 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8351 (ptm160)
REVERT: A  324 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7811 (p0)
REVERT: A  350 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7089 (pmm)
REVERT: A  486 MET cc_start: 0.8105 (ttp) cc_final: 0.7760 (tpt)
REVERT: A  829 LEU cc_start: 0.7167 (mt) cc_final: 0.6544 (mp)
REVERT: B   14 PHE cc_start: 0.8769 (m-10) cc_final: 0.8542 (m-80)
REVERT: B   32 ARG cc_start: 0.8244 (tpp-160) cc_final: 0.7299 (tpp-160)
REVERT: B  124 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8613 (tm-30)
REVERT: B  128 ARG cc_start: 0.9226 (mmt90) cc_final: 0.8995 (mmm-85)
REVERT: B  194 TYR cc_start: 0.4964 (m-80) cc_final: 0.4315 (m-80)
REVERT: D   87 ARG cc_start: 0.7557 (mtp180) cc_final: 0.6994 (mtp180)
REVERT: D  198 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9069 (mp)
REVERT: E    1 MET cc_start: 0.7373 (mmt) cc_final: 0.6953 (mmt)
REVERT: E  125 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8789 (tm-30)
  outliers start: 56
  outliers final: 33
  residues processed: 251
  average time/residue: 0.1207
  time to fit residues: 44.6823
Evaluate side-chains
  201 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 165
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   27 ARG
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  356 MET
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain A residue  622 VAL
Chi-restraints excluded: chain A residue  729 THR
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue  179 ASN
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  195 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 60 optimal weight:    0.4980
   chunk 39 optimal weight:    0.6980
   chunk 98 optimal weight:    9.9990
   chunk 115 optimal weight:    1.9990
   chunk 31 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 152 optimal weight:    6.9990
   chunk 97 optimal weight:   20.0000
   chunk 77 optimal weight:    6.9990
   chunk 151 optimal weight:    5.9990
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 321 ASN
** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 125 GLN ** 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 = 0.3986 r_free = 0.3986 target = 0.106770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.079288 restraints weight = 48325.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.081875 restraints weight = 28189.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.083643 restraints weight = 19797.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 61)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.084847 restraints weight = 15591.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.085596 restraints weight = 13274.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14074  Z= 0.177
  Angle     :  0.618   9.804  19253  Z= 0.330
  Chirality :  0.044   0.256   2120
  Planarity :  0.004   0.048   2287
  Dihedral  : 18.060 164.129   2371
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 16.63 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.21), residues: 1574
  helix:  0.86 (0.22), residues: 542
  sheet: -0.27 (0.26), residues: 375
  loop : -0.77 (0.25), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 128 
 TYR   0.019   0.002   TYR B  39 
 PHE   0.018   0.001   PHE A 651 
 TRP   0.011   0.002   TRP B  92 
 HIS   0.003   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (14074)
  covalent geometry    : angle       0.61809 (19253)
  hydrogen bonds       : bond        0.04076 (  681)
  hydrogen bonds       : angle       5.33826 ( 1863)

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

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

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 178
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.4307 (ptt) cc_final: 0.3114 (ppp)
REVERT: A   85 ASP cc_start: 0.8550 (t0) cc_final: 0.8276 (t70)
REVERT: A  236 MET cc_start: 0.7697 (mtp) cc_final: 0.7202 (mpp)
REVERT: A  238 ARG cc_start: 0.8681 (mtp-110) cc_final: 0.8324 (ptm160)
REVERT: A  246 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8380 (mmtt)
REVERT: A  486 MET cc_start: 0.8240 (ttp) cc_final: 0.7589 (mmm)
REVERT: A  665 ARG cc_start: 0.8631 (mmm160) cc_final: 0.8369 (mmm-85)
REVERT: A  671 MET cc_start: 0.8142 (tpp) cc_final: 0.7869 (tpp)
REVERT: A  721 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7236 (p-80)
REVERT: A  727 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7546 (mtt)
REVERT: B   14 PHE cc_start: 0.8809 (m-10) cc_final: 0.8564 (m-80)
REVERT: B   32 ARG cc_start: 0.8219 (tpp-160) cc_final: 0.7292 (tpp-160)
REVERT: B  124 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8617 (tm-30)
REVERT: B  128 ARG cc_start: 0.9240 (mmt90) cc_final: 0.9002 (mmm-85)
REVERT: D   87 ARG cc_start: 0.7520 (mtp180) cc_final: 0.7114 (mtp180)
REVERT: E  125 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8780 (tm-30)
REVERT: E  189 MET cc_start: 0.9207 (mpp) cc_final: 0.8953 (mpp)
  outliers start: 61
  outliers final: 47
  residues processed: 227
  average time/residue: 0.1192
  time to fit residues: 39.7094
Evaluate side-chains
  214 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 164
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   27 ARG
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  356 MET
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  721 HIS
Chi-restraints excluded: chain A residue  724 ILE
Chi-restraints excluded: chain A residue  727 MET
Chi-restraints excluded: chain A residue  729 THR
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  790 ASP
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  147 ILE
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   73 ILE
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  131 ARG
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain D residue  158 SER
Chi-restraints excluded: chain D residue  179 ASN
Chi-restraints excluded: chain D residue  189 MET
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  217 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 88 optimal weight:    0.3980
   chunk 120 optimal weight:    1.9990
   chunk 123 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 105 optimal weight:    6.9990
   chunk 93 optimal weight:   30.0000
   chunk 147 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   chunk 71 optimal weight:    6.9990
   overall best weight:    3.2788

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 125 GLN ** 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 = 0.3968 r_free = 0.3968 target = 0.105535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.079823 restraints weight = 48550.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.081285 restraints weight = 28808.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.082070 restraints weight = 20316.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.082513 restraints weight = 18556.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.083189 restraints weight = 16593.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  14074  Z= 0.210
  Angle     :  0.657  11.901  19253  Z= 0.344
  Chirality :  0.044   0.235   2120
  Planarity :  0.004   0.046   2287
  Dihedral  : 18.050 158.501   2364
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 16.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 18.10 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.34 (0.21), residues: 1574
  helix:  0.70 (0.22), residues: 549
  sheet: -0.46 (0.25), residues: 388
  loop : -0.77 (0.25), residues: 637

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E 162 
 TYR   0.019   0.002   TYR B  39 
 PHE   0.023   0.001   PHE B 109 
 TRP   0.014   0.002   TRP A 593 
 HIS   0.003   0.001   HIS D 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 (14074)
  covalent geometry    : angle       0.65659 (19253)
  hydrogen bonds       : bond        0.04134 (  681)
  hydrogen bonds       : angle       5.35017 ( 1863)

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

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

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 175
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.4420 (ptt) cc_final: 0.3335 (ppp)
REVERT: A   70 MET cc_start: 0.8555 (mpp) cc_final: 0.8041 (mpp)
REVERT: A   85 ASP cc_start: 0.8724 (t0) cc_final: 0.8373 (t70)
REVERT: A  188 PHE cc_start: 0.7828 (m-80) cc_final: 0.7603 (m-80)
REVERT: A  196 MET cc_start: 0.8810 (mpp) cc_final: 0.8470 (mpp)
REVERT: A  236 MET cc_start: 0.7836 (mtp) cc_final: 0.7285 (mpp)
REVERT: A  238 ARG cc_start: 0.8716 (mtp-110) cc_final: 0.8366 (ptm160)
REVERT: A  246 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8427 (mmtt)
REVERT: A  350 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7381 (pmm)
REVERT: A  486 MET cc_start: 0.8200 (ttp) cc_final: 0.7602 (mmm)
REVERT: A  671 MET cc_start: 0.8305 (tpp) cc_final: 0.8059 (tpp)
REVERT: A  721 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.7289 (p-80)
REVERT: A  727 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7388 (mtt)
REVERT: A  881 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8559 (pp20)
REVERT: A  885 MET cc_start: 0.8192 (mmt) cc_final: 0.7924 (mmt)
REVERT: B   14 PHE cc_start: 0.8827 (m-10) cc_final: 0.8621 (m-80)
REVERT: B   32 ARG cc_start: 0.8174 (tpp-160) cc_final: 0.7814 (tpp-160)
REVERT: D   82 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8485 (ptpp)
REVERT: D  116 THR cc_start: 0.8419 (t) cc_final: 0.8201 (m)
REVERT: E  125 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8875 (tm-30)
REVERT: E  187 MET cc_start: 0.9010 (mmm) cc_final: 0.8294 (mmt)
  outliers start: 68
  outliers final: 46
  residues processed: 227
  average time/residue: 0.1197
  time to fit residues: 40.2179
Evaluate side-chains
  212 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 160
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   27 ARG
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  299 LYS
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  356 MET
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  589 VAL
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  721 HIS
Chi-restraints excluded: chain A residue  727 MET
Chi-restraints excluded: chain A residue  729 THR
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain D residue   82 LYS
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  131 ARG
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain D residue  158 SER
Chi-restraints excluded: chain D residue  179 ASN
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  217 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 124 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 141 optimal weight:    3.9990
   chunk 84 optimal weight:    0.8980
   chunk 152 optimal weight:    3.9990
   chunk 138 optimal weight:    9.9990
   chunk 88 optimal weight:    2.9990
   chunk 93 optimal weight:    8.9990
   chunk 111 optimal weight:    3.9990
   chunk 125 optimal weight:    0.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 183 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.107780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.080511 restraints weight = 47647.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.083201 restraints weight = 27496.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.084995 restraints weight = 19079.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 60)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.086264 restraints weight = 14944.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.087069 restraints weight = 12632.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  14074  Z= 0.134
  Angle     :  0.630  13.089  19253  Z= 0.325
  Chirality :  0.044   0.254   2120
  Planarity :  0.004   0.046   2287
  Dihedral  : 17.902 153.305   2364
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 14.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 19.43 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.21), residues: 1574
  helix:  0.80 (0.22), residues: 548
  sheet: -0.31 (0.25), residues: 406
  loop : -0.65 (0.26), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 128 
 TYR   0.014   0.001   TYR B  39 
 PHE   0.017   0.001   PHE A 651 
 TRP   0.016   0.001   TRP B  92 
 HIS   0.003   0.001   HIS A 721 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (14074)
  covalent geometry    : angle       0.62999 (19253)
  hydrogen bonds       : bond        0.03604 (  681)
  hydrogen bonds       : angle       5.11847 ( 1863)

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

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

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 180
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.4063 (ptt) cc_final: 0.3032 (ppp)
REVERT: A   85 ASP cc_start: 0.8552 (t0) cc_final: 0.8295 (t70)
REVERT: A  236 MET cc_start: 0.7691 (mtp) cc_final: 0.7202 (mpp)
REVERT: A  238 ARG cc_start: 0.8667 (mtp-110) cc_final: 0.8277 (ptm160)
REVERT: A  246 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8313 (mmtt)
REVERT: A  324 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7893 (p0)
REVERT: A  350 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7252 (pmm)
REVERT: A  486 MET cc_start: 0.8194 (ttp) cc_final: 0.7542 (mmm)
REVERT: A  721 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7203 (p-80)
REVERT: A  727 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7494 (mtm)
REVERT: A  881 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8440 (pp20)
REVERT: A  885 MET cc_start: 0.8143 (mmt) cc_final: 0.7902 (mmt)
REVERT: B   14 PHE cc_start: 0.8833 (m-10) cc_final: 0.8623 (m-80)
REVERT: B   32 ARG cc_start: 0.8172 (tpp-160) cc_final: 0.7296 (tpp-160)
REVERT: B   50 PHE cc_start: 0.6640 (p90) cc_final: 0.5850 (p90)
REVERT: D   87 ARG cc_start: 0.7250 (mtp180) cc_final: 0.6939 (mtp180)
REVERT: E    1 MET cc_start: 0.7341 (mmt) cc_final: 0.6772 (mmt)
REVERT: E  125 GLN cc_start: 0.9117 (tm-30) cc_final: 0.8731 (tm-30)
REVERT: E  184 MET cc_start: 0.8970 (mmm) cc_final: 0.8751 (mmm)
  outliers start: 59
  outliers final: 42
  residues processed: 226
  average time/residue: 0.1217
  time to fit residues: 40.4410
Evaluate side-chains
  207 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 159
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   27 ARG
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  356 MET
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  721 HIS
Chi-restraints excluded: chain A residue  727 MET
Chi-restraints excluded: chain A residue  729 THR
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain B residue   31 THR
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   55 TYR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue  131 ARG
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  217 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 148 optimal weight:    0.6980
   chunk 152 optimal weight:    8.9990
   chunk 93 optimal weight:   30.0000
   chunk 74 optimal weight:    3.9990
   chunk 110 optimal weight:    5.9990
   chunk 127 optimal weight:    4.9990
   chunk 112 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 90 optimal weight:    9.9990
   overall best weight:    3.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 ASN
** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 125 GLN ** 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 = 0.3964 r_free = 0.3964 target = 0.105300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.079352 restraints weight = 48526.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.081045 restraints weight = 29103.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.081474 restraints weight = 20655.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.082004 restraints weight = 19060.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.082105 restraints weight = 16795.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  14074  Z= 0.215
  Angle     :  0.675  10.881  19253  Z= 0.352
  Chirality :  0.045   0.221   2120
  Planarity :  0.004   0.041   2287
  Dihedral  : 17.915 153.419   2360
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 17.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 18.98 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.21), residues: 1574
  helix:  0.70 (0.22), residues: 548
  sheet: -0.38 (0.25), residues: 396
  loop : -0.79 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 128 
 TYR   0.019   0.002   TYR B  39 
 PHE   0.013   0.001   PHE A 868 
 TRP   0.014   0.002   TRP B  92 
 HIS   0.003   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (14074)
  covalent geometry    : angle       0.67493 (19253)
  hydrogen bonds       : bond        0.04140 (  681)
  hydrogen bonds       : angle       5.30315 ( 1863)

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

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

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 169
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.4282 (ptt) cc_final: 0.3169 (ppp)
REVERT: A   70 MET cc_start: 0.8489 (mpp) cc_final: 0.7983 (mpp)
REVERT: A   83 MET cc_start: 0.6797 (tpp) cc_final: 0.6586 (tpp)
REVERT: A   85 ASP cc_start: 0.8680 (t0) cc_final: 0.8312 (t70)
REVERT: A  236 MET cc_start: 0.7863 (mtp) cc_final: 0.7314 (mpp)
REVERT: A  246 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8434 (mmtt)
REVERT: A  350 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7286 (pmm)
REVERT: A  486 MET cc_start: 0.8136 (ttp) cc_final: 0.7581 (mmm)
REVERT: A  671 MET cc_start: 0.7992 (tpp) cc_final: 0.7664 (tpp)
REVERT: A  721 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7165 (p-80)
REVERT: A  727 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7475 (mtt)
REVERT: A  881 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8507 (pp20)
REVERT: A  885 MET cc_start: 0.8380 (mmt) cc_final: 0.8039 (mmt)
REVERT: B   30 MET cc_start: 0.8046 (mmm) cc_final: 0.7748 (mmm)
REVERT: B   32 ARG cc_start: 0.8201 (tpp-160) cc_final: 0.7220 (tpp-160)
REVERT: B   50 PHE cc_start: 0.6677 (p90) cc_final: 0.6138 (p90)
REVERT: E  125 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8775 (tm-30)
REVERT: E  187 MET cc_start: 0.8829 (mpp) cc_final: 0.8409 (mpp)
REVERT: E  189 MET cc_start: 0.9041 (mpp) cc_final: 0.8174 (mpp)
  outliers start: 73
  outliers final: 54
  residues processed: 225
  average time/residue: 0.1218
  time to fit residues: 40.4454
Evaluate side-chains
  218 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 159
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   27 ARG
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  356 MET
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  589 VAL
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  721 HIS
Chi-restraints excluded: chain A residue  727 MET
Chi-restraints excluded: chain A residue  729 THR
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  785 ILE
Chi-restraints excluded: chain A residue  790 ASP
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   55 TYR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  131 ARG
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain D residue  189 MET
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  217 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 108 optimal weight:   20.0000
   chunk 70 optimal weight:    0.5980
   chunk 111 optimal weight:    0.8980
   chunk 95 optimal weight:    5.9990
   chunk 43 optimal weight:    7.9990
   chunk 73 optimal weight:    0.6980
   chunk 106 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 159 optimal weight:   10.0000
   chunk 63 optimal weight:    4.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 603 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 = 0.4013 r_free = 0.4013 target = 0.108273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.082741 restraints weight = 47919.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.085079 restraints weight = 27994.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.085639 restraints weight = 18838.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.086077 restraints weight = 17177.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.086252 restraints weight = 15126.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14074  Z= 0.131
  Angle     :  0.651  13.378  19253  Z= 0.332
  Chirality :  0.044   0.251   2120
  Planarity :  0.004   0.042   2287
  Dihedral  : 17.809 153.276   2360
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 20.82 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.21), residues: 1574
  helix:  0.76 (0.22), residues: 548
  sheet: -0.28 (0.25), residues: 406
  loop : -0.68 (0.26), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 128 
 TYR   0.015   0.001   TYR B  39 
 PHE   0.018   0.001   PHE B  28 
 TRP   0.020   0.002   TRP B  92 
 HIS   0.003   0.001   HIS B 213 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (14074)
  covalent geometry    : angle       0.65133 (19253)
  hydrogen bonds       : bond        0.03498 (  681)
  hydrogen bonds       : angle       5.08567 ( 1863)

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

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

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 176
  time to evaluate  : 0.533 
Fit side-chains
REVERT: A   37 MET cc_start: 0.4179 (ptt) cc_final: 0.3052 (ppp)
REVERT: A   63 MET cc_start: 0.8515 (mmt) cc_final: 0.8303 (mmp)
REVERT: A   85 ASP cc_start: 0.8600 (t0) cc_final: 0.8283 (t0)
REVERT: A  136 TYR cc_start: 0.7307 (t80) cc_final: 0.6965 (t80)
REVERT: A  226 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8557 (tpp80)
REVERT: A  236 MET cc_start: 0.7802 (mtp) cc_final: 0.7267 (mpp)
REVERT: A  238 ARG cc_start: 0.8713 (mtp-110) cc_final: 0.8349 (ptm160)
REVERT: A  246 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8182 (mtmm)
REVERT: A  288 GLU cc_start: 0.8004 (mp0) cc_final: 0.7627 (mp0)
REVERT: A  324 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7965 (p0)
REVERT: A  350 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7170 (pmm)
REVERT: A  486 MET cc_start: 0.8094 (ttp) cc_final: 0.7576 (mmm)
REVERT: A  721 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7129 (p-80)
REVERT: A  727 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7517 (mtm)
REVERT: A  881 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8434 (pp20)
REVERT: A  885 MET cc_start: 0.8192 (mmt) cc_final: 0.7981 (mmt)
REVERT: B   32 ARG cc_start: 0.8200 (tpp-160) cc_final: 0.7098 (tpp-160)
REVERT: B  128 ARG cc_start: 0.9185 (mmt90) cc_final: 0.8982 (mmm-85)
REVERT: D   87 ARG cc_start: 0.7410 (mmm160) cc_final: 0.7041 (mmm160)
REVERT: E    1 MET cc_start: 0.7375 (mmt) cc_final: 0.6861 (mmt)
REVERT: E  125 GLN cc_start: 0.9118 (tm-30) cc_final: 0.8845 (tm-30)
REVERT: E  187 MET cc_start: 0.8944 (mpp) cc_final: 0.8714 (mpp)
REVERT: E  189 MET cc_start: 0.8999 (mpp) cc_final: 0.8263 (mpp)
  outliers start: 52
  outliers final: 39
  residues processed: 216
  average time/residue: 0.1230
  time to fit residues: 39.1669
Evaluate side-chains
  207 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 161
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   27 ARG
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  356 MET
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  721 HIS
Chi-restraints excluded: chain A residue  727 MET
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   55 TYR
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue  131 ARG
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  217 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 133 optimal weight:    9.9990
   chunk 148 optimal weight:    9.9990
   chunk 22 optimal weight:    1.9990
   chunk 142 optimal weight:    0.1980
   chunk 154 optimal weight:    9.9990
   chunk 54 optimal weight:    9.9990
   chunk 26 optimal weight:    8.9990
   chunk 103 optimal weight:    7.9990
   chunk 45 optimal weight:    7.9990
   chunk 46 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    2.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 ASN
** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 124 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.105588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.079771 restraints weight = 48577.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.081442 restraints weight = 29232.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.081937 restraints weight = 20678.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.082447 restraints weight = 18962.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.082570 restraints weight = 16585.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14074  Z= 0.197
  Angle     :  0.693  13.208  19253  Z= 0.353
  Chirality :  0.045   0.271   2120
  Planarity :  0.004   0.040   2287
  Dihedral  : 17.820 153.677   2355
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 17.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 21.27 %
    Favored  : 74.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.21), residues: 1574
  helix:  0.62 (0.22), residues: 548
  sheet: -0.27 (0.25), residues: 396
  loop : -0.71 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 162 
 TYR   0.018   0.002   TYR B  39 
 PHE   0.021   0.001   PHE B  50 
 TRP   0.019   0.002   TRP B  92 
 HIS   0.003   0.001   HIS A 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (14074)
  covalent geometry    : angle       0.69275 (19253)
  hydrogen bonds       : bond        0.03920 (  681)
  hydrogen bonds       : angle       5.22393 ( 1863)

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

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

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 159
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.4275 (ptt) cc_final: 0.3106 (ppp)
REVERT: A   63 MET cc_start: 0.8511 (mmt) cc_final: 0.8293 (mmp)
REVERT: A   70 MET cc_start: 0.8619 (mpp) cc_final: 0.8036 (mpp)
REVERT: A   85 ASP cc_start: 0.8677 (t0) cc_final: 0.8406 (t70)
REVERT: A  236 MET cc_start: 0.7848 (mtp) cc_final: 0.7317 (mpp)
REVERT: A  246 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8240 (mtmm)
REVERT: A  288 GLU cc_start: 0.8067 (mp0) cc_final: 0.7656 (mp0)
REVERT: A  350 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7258 (pmm)
REVERT: A  459 MET cc_start: 0.6172 (mpp) cc_final: 0.5906 (mpp)
REVERT: A  486 MET cc_start: 0.8136 (ttp) cc_final: 0.7585 (mmm)
REVERT: A  501 MET cc_start: 0.7877 (ppp) cc_final: 0.7473 (ppp)
REVERT: A  721 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7149 (p-80)
REVERT: A  727 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7461 (mtt)
REVERT: A  844 TRP cc_start: 0.8698 (OUTLIER) cc_final: 0.7712 (p-90)
REVERT: A  881 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8485 (pp20)
REVERT: A  885 MET cc_start: 0.8324 (mmt) cc_final: 0.8056 (mmt)
REVERT: B   30 MET cc_start: 0.8029 (mmm) cc_final: 0.7812 (mmm)
REVERT: B   32 ARG cc_start: 0.8174 (tpp-160) cc_final: 0.7193 (tpp-160)
REVERT: B  128 ARG cc_start: 0.9189 (mmt90) cc_final: 0.8987 (mmm-85)
REVERT: D   87 ARG cc_start: 0.7442 (mmm160) cc_final: 0.6923 (mtp180)
REVERT: E    1 MET cc_start: 0.7490 (mmt) cc_final: 0.6974 (mmt)
REVERT: E   41 GLU cc_start: 0.8301 (pm20) cc_final: 0.7626 (pm20)
REVERT: E  187 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8538 (mpp)
REVERT: E  189 MET cc_start: 0.9063 (mpp) cc_final: 0.8359 (mpp)
  outliers start: 57
  outliers final: 47
  residues processed: 202
  average time/residue: 0.1206
  time to fit residues: 35.9296
Evaluate side-chains
  208 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 154
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   27 ARG
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  209 ILE
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  356 MET
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  490 GLU
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  721 HIS
Chi-restraints excluded: chain A residue  727 MET
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  844 TRP
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   55 TYR
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  131 ARG
Chi-restraints excluded: chain D residue  158 SER
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  187 MET
Chi-restraints excluded: chain E residue  217 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 124 optimal weight:    3.9990
   chunk 155 optimal weight:   10.0000
   chunk 103 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 101 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 143 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 603 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 = 0.4011 r_free = 0.4011 target = 0.108059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.082498 restraints weight = 48507.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.084665 restraints weight = 28540.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.085293 restraints weight = 19391.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.085721 restraints weight = 17590.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.085855 restraints weight = 15594.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14074  Z= 0.135
  Angle     :  0.670  12.782  19253  Z= 0.337
  Chirality :  0.045   0.205   2120
  Planarity :  0.004   0.042   2287
  Dihedral  : 17.755 153.925   2355
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 14.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 22.22 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.21), residues: 1574
  helix:  0.64 (0.22), residues: 550
  sheet: -0.26 (0.25), residues: 401
  loop : -0.72 (0.26), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 162 
 TYR   0.016   0.001   TYR B  39 
 PHE   0.018   0.001   PHE B  28 
 TRP   0.023   0.002   TRP B  92 
 HIS   0.002   0.001   HIS A 721 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (14074)
  covalent geometry    : angle       0.66956 (19253)
  hydrogen bonds       : bond        0.03466 (  681)
  hydrogen bonds       : angle       5.06059 ( 1863)

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

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

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 167
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 MET cc_start: 0.4279 (ptt) cc_final: 0.3123 (ppp)
REVERT: A   63 MET cc_start: 0.8495 (mmt) cc_final: 0.8249 (mmp)
REVERT: A   70 MET cc_start: 0.8526 (mpp) cc_final: 0.7973 (mpp)
REVERT: A   85 ASP cc_start: 0.8559 (t0) cc_final: 0.8336 (t70)
REVERT: A  136 TYR cc_start: 0.7298 (t80) cc_final: 0.6951 (t80)
REVERT: A  226 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8561 (tpp80)
REVERT: A  236 MET cc_start: 0.7787 (mtp) cc_final: 0.7291 (mpp)
REVERT: A  238 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8375 (ptm160)
REVERT: A  246 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8187 (mtmm)
REVERT: A  288 GLU cc_start: 0.8009 (mp0) cc_final: 0.7636 (mp0)
REVERT: A  350 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7165 (pmm)
REVERT: A  459 MET cc_start: 0.6375 (mpp) cc_final: 0.6147 (mpp)
REVERT: A  486 MET cc_start: 0.8102 (ttp) cc_final: 0.7589 (mmm)
REVERT: A  501 MET cc_start: 0.7894 (ppp) cc_final: 0.7516 (ppp)
REVERT: A  721 HIS cc_start: 0.7947 (OUTLIER) cc_final: 0.7137 (p-80)
REVERT: A  881 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8431 (pp20)
REVERT: B   30 MET cc_start: 0.7949 (mmm) cc_final: 0.7736 (mmm)
REVERT: B   32 ARG cc_start: 0.8178 (tpp-160) cc_final: 0.7151 (tpp-160)
REVERT: D   87 ARG cc_start: 0.7457 (mmm160) cc_final: 0.7087 (mmm160)
REVERT: E    1 MET cc_start: 0.7468 (mmt) cc_final: 0.7040 (mmt)
REVERT: E  125 GLN cc_start: 0.9070 (tm-30) cc_final: 0.8759 (tm-30)
REVERT: E  189 MET cc_start: 0.8997 (mpp) cc_final: 0.8355 (mpp)
  outliers start: 50
  outliers final: 39
  residues processed: 204
  average time/residue: 0.1241
  time to fit residues: 37.1121
Evaluate side-chains
  204 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 160
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   27 ARG
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  356 MET
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  721 HIS
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   55 TYR
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  131 ARG
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  217 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 8 optimal weight:   20.0000
   chunk 52 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 116 optimal weight:    1.9990
   chunk 140 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 34 optimal weight:    8.9990
   chunk 2 optimal weight:    7.9990
   chunk 18 optimal weight:    0.8980
   chunk 90 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 ASN
** A 603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 124 GLN ** 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 = 0.3978 r_free = 0.3978 target = 0.106134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.080275 restraints weight = 48707.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.082028 restraints weight = 29362.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.082710 restraints weight = 21220.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.083168 restraints weight = 18229.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.083300 restraints weight = 16308.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14074  Z= 0.188
  Angle     :  0.693  12.039  19253  Z= 0.353
  Chirality :  0.045   0.220   2120
  Planarity :  0.004   0.040   2287
  Dihedral  : 17.805 154.183   2354
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 17.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 22.66 %
    Favored  : 73.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.21), residues: 1574
  helix:  0.64 (0.22), residues: 543
  sheet: -0.34 (0.25), residues: 398
  loop : -0.71 (0.25), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 162 
 TYR   0.018   0.002   TYR B  39 
 PHE   0.016   0.001   PHE A 367 
 TRP   0.024   0.002   TRP B  92 
 HIS   0.003   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (14074)
  covalent geometry    : angle       0.69346 (19253)
  hydrogen bonds       : bond        0.03821 (  681)
  hydrogen bonds       : angle       5.19381 ( 1863)

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

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

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3148 Ramachandran restraints generated.
    1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 161
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 MET cc_start: 0.8498 (mmt) cc_final: 0.8284 (mmp)
REVERT: A   70 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7946 (mpp)
REVERT: A  236 MET cc_start: 0.7818 (mtp) cc_final: 0.7342 (mpp)
REVERT: A  238 ARG cc_start: 0.8734 (mtp-110) cc_final: 0.8093 (mmp80)
REVERT: A  246 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8257 (mtmm)
REVERT: A  288 GLU cc_start: 0.8069 (mp0) cc_final: 0.7671 (mp0)
REVERT: A  350 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7214 (pmm)
REVERT: A  459 MET cc_start: 0.6415 (mpp) cc_final: 0.6211 (mpp)
REVERT: A  486 MET cc_start: 0.8124 (ttp) cc_final: 0.7580 (mmm)
REVERT: A  501 MET cc_start: 0.7918 (ppp) cc_final: 0.7544 (ppp)
REVERT: A  721 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7118 (p-80)
REVERT: A  881 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8487 (pp20)
REVERT: D   87 ARG cc_start: 0.7492 (mmm160) cc_final: 0.6988 (mtp180)
REVERT: E    1 MET cc_start: 0.7386 (mmt) cc_final: 0.6922 (mmt)
REVERT: E  189 MET cc_start: 0.9095 (mpp) cc_final: 0.8414 (mpp)
  outliers start: 49
  outliers final: 42
  residues processed: 197
  average time/residue: 0.1262
  time to fit residues: 36.2967
Evaluate side-chains
  203 residues out of total 1359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 156
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   27 ARG
Chi-restraints excluded: chain A residue   70 MET
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  226 ARG
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  285 PHE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  350 MET
Chi-restraints excluded: chain A residue  356 MET
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  421 ASN
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  467 ILE
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  548 LEU
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  614 ILE
Chi-restraints excluded: chain A residue  676 HIS
Chi-restraints excluded: chain A residue  721 HIS
Chi-restraints excluded: chain A residue  749 ILE
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  817 VAL
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  862 ILE
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   47 VAL
Chi-restraints excluded: chain B residue   55 TYR
Chi-restraints excluded: chain B residue  140 ILE
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue  129 VAL
Chi-restraints excluded: chain D residue  131 ARG
Chi-restraints excluded: chain D residue  138 ILE
Chi-restraints excluded: chain D residue  198 LEU
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain E residue  100 VAL
Chi-restraints excluded: chain E residue  152 PHE
Chi-restraints excluded: chain E residue  217 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 147 optimal weight:   10.0000
   chunk 48 optimal weight:   10.0000
   chunk 42 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 81 optimal weight:    7.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
** A  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 421 ASN
A 603 ASN
E  13 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.106879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.081002 restraints weight = 48936.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.083033 restraints weight = 28803.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.083566 restraints weight = 19817.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.084041 restraints weight = 18105.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.084230 restraints weight = 16038.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14074  Z= 0.150
  Angle     :  0.695  13.187  19253  Z= 0.354
  Chirality :  0.045   0.223   2120
  Planarity :  0.004   0.042   2287
  Dihedral  : 17.801 154.397   2354
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 17.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 22.66 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.21), residues: 1574
  helix:  0.60 (0.22), residues: 543
  sheet: -0.32 (0.25), residues: 398
  loop : -0.69 (0.25), residues: 633

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 162 
 TYR   0.020   0.002   TYR B  39 
 PHE   0.018   0.001   PHE B  28 
 TRP   0.024   0.001   TRP B  92 
 HIS   0.003   0.001   HIS A 721 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (14074)
  covalent geometry    : angle       0.69519 (19253)
  hydrogen bonds       : bond        0.03733 (  681)
  hydrogen bonds       : angle       5.13359 ( 1863)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2477.51 seconds
wall clock time: 43 minutes 54.30 seconds (2634.30 seconds total)