Starting phenix.real_space_refine
on Thu Jul  2 05:46:58 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8iww_35781/07_2026/8iww_35781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iww_35781/07_2026/8iww_35781.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.71
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iww_35781/07_2026/8iww_35781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iww_35781/07_2026/8iww_35781.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8iww_35781/07_2026/8iww_35781.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8iww_35781/07_2026/8iww_35781.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iww_35781/07_2026/8iww_35781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iww_35781/07_2026/8iww_35781.cif"
  }
  resolution = 3.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.015
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: 8
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     Al      1      5.89       5
     P       2      5.49       5
     S      52      5.16       5
     C    4355      2.51       5
     N    1145      2.21       5
     O    1288      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6848
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 890, 6815
          Classifications: {'peptide': 890}
          Link IDs: {'PTRANS': 35, 'TRANS': 854}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' CA': 1, 'ADP': 1, 'ALF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.54, per 1000 atoms: 0.22
  Number of scatterers: 6848
  At special positions: 0
  Unit cell: (115.92, 100.8, 107.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     Ca      1     19.99
     S      52     16.00
     P       2     15.00
     Al      1     13.00
     F       4      9.00
     O    1288      8.00
     N    1145      7.00
     C    4355      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 370.2 milliseconds
  

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1658

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 8 sheets defined
      52.8% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 29
    Processing helix  chain 'A' and resid 30 through 39
    Processing helix  chain 'A' and resid 47 through 59
    Processing helix  chain 'A' and resid 70 through 78
    Processing helix  chain 'A' and resid 81 through 97
    Processing helix  chain 'A' and resid 100 through 130
    Processing helix  chain 'A' and resid 239 through 249
    Processing helix  chain 'A' and resid 256 through 286
    Processing helix  chain 'A' and resid 290 through 306
      removed outlier: 3.724A  pdb=" N   ILE A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 328
    Processing helix  chain 'A' and resid 335 through 341
      removed outlier: 3.981A  pdb=" N   GLU A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   THR A 340 " --> pdb=" O   PRO A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 411
      removed outlier: 3.514A  pdb=" N   ILE A 404 " --> pdb=" O   ALA A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 437
      removed outlier: 3.719A  pdb=" N   LEU A 430 " --> pdb=" O   THR A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 444
      removed outlier: 3.763A  pdb=" N   LEU A 442 " --> pdb=" O   LEU A 439 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLN A 443 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   GLN A 444 " --> pdb=" O   GLY A 441 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 439 through 444'
    Processing helix  chain 'A' and resid 482 through 487
    Processing helix  chain 'A' and resid 503 through 520
      removed outlier: 3.744A  pdb=" N   ALA A 520 " --> pdb=" O   ARG A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 561
      removed outlier: 3.508A  pdb=" N   ALA A 555 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 584
      removed outlier: 3.554A  pdb=" N   ALA A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 601
      removed outlier: 3.881A  pdb=" N   ILE A 599 " --> pdb=" O   SER A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 608
    Processing helix  chain 'A' and resid 621 through 633
      removed outlier: 3.745A  pdb=" N   MET A 626 " --> pdb=" O   PRO A 622 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LYS A 627 " --> pdb=" O   ARG A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 655
    Processing helix  chain 'A' and resid 667 through 672
      removed outlier: 3.668A  pdb=" N   ALA A 672 " --> pdb=" O   VAL A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 721
      removed outlier: 4.056A  pdb=" N   MET A 686 " --> pdb=" O   PHE A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 742
    Processing helix  chain 'A' and resid 743 through 748
    Processing helix  chain 'A' and resid 757 through 761
      removed outlier: 3.566A  pdb=" N   ARG A 760 " --> pdb=" O   ASP A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 798
      removed outlier: 3.914A  pdb=" N   LEU A 798 " --> pdb=" O   PHE A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 826
      removed outlier: 3.576A  pdb=" N   THR A 808 " --> pdb=" O   THR A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 860
    Processing helix  chain 'A' and resid 861 through 866
      removed outlier: 3.663A  pdb=" N   LYS A 866 " --> pdb=" O   PRO A 862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 874 through 909
      removed outlier: 4.061A  pdb=" N   SER A 886 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)
      removed outlier: 5.259A  pdb=" N   SER A 887 " --> pdb=" O   GLY A 883 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   VAL A 888 " --> pdb=" O   LEU A 884 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   CYS A 889 " --> pdb=" O   THR A 885 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL A 909 " --> pdb=" O   ILE A 905 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 146 through 151
      removed outlier: 5.268A  pdb=" N   HIS A 140 " --> pdb=" O   CYS A 162 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   CYS A 162 " --> pdb=" O   HIS A 140 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   THR A 160 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   SER A 182 " --> pdb=" O   ARG A 224 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLY A 226 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ASP A 180 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ALA A 228 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA A 178 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   GLY A 230 " --> pdb=" O   PHE A 176 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   PHE A 176 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   VAL A 232 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   ARG A 174 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY A 234 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ILE A 183 " --> pdb=" O   CYS A 195 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   CYS A 195 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 151
      removed outlier: 5.268A  pdb=" N   HIS A 140 " --> pdb=" O   CYS A 162 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   CYS A 162 " --> pdb=" O   HIS A 140 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   THR A 160 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   SER A 182 " --> pdb=" O   ARG A 224 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   GLY A 226 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ASP A 180 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ALA A 228 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA A 178 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   GLY A 230 " --> pdb=" O   PHE A 176 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   PHE A 176 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   VAL A 232 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   ARG A 174 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY A 234 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 565 through 566
      removed outlier: 7.143A  pdb=" N   VAL A 346 " --> pdb=" O   ALA A 640 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE A 657 " --> pdb=" O   VAL A 639 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 361 through 362
      removed outlier: 7.169A  pdb=" N   LEU A 527 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   LEU A 541 " --> pdb=" O   LEU A 525 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   LEU A 525 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   GLY A 543 " --> pdb=" O   ARG A 523 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   ARG A 523 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   ALA A 462 " --> pdb=" O   GLU A 451 " (cutoff:3.500A)
      removed outlier: 4.694A  pdb=" N   GLU A 451 " --> pdb=" O   ALA A 462 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   LYS A 464 " --> pdb=" O   LYS A 449 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 393
      removed outlier: 4.422A  pdb=" N   VAL A 386 " --> pdb=" O   VAL A 393 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   HIS A 364 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 7.432A  pdb=" N   PHE A 538 " --> pdb=" O   THR A 491 " (cutoff:3.500A)
      removed outlier: 5.538A  pdb=" N   TYR A 493 " --> pdb=" O   PHE A 538 " (cutoff:3.500A)
      removed outlier: 10.073A  pdb=" N   GLY A 540 " --> pdb=" O   TYR A 493 " (cutoff:3.500A)
      removed outlier: 12.844A  pdb=" N   SER A 495 " --> pdb=" O   GLY A 540 " (cutoff:3.500A)
      removed outlier: 18.667A  pdb=" N   VAL A 542 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 415 through 417
    Processing sheet with id=AA7, first strand: chain 'A' and resid 592 through 594
      removed outlier: 8.174A  pdb=" N   GLN A 592 " --> pdb=" O   ALA A 615 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   PHE A 617 " --> pdb=" O   GLN A 592 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   VAL A 594 " --> pdb=" O   PHE A 617 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 660 through 661
      removed outlier: 6.560A  pdb=" N   ALA A 660 " --> pdb=" O   LEU A 677 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    392 hydrogen bonds defined for protein.
    1137 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2204
        1.34 -     1.46: 804
        1.46 -     1.57: 3858
        1.57 -     1.69: 3
        1.69 -     1.81: 88
  Bond restraints: 6957
  Sorted by residual:
  bond pdb=" F3  ALF A1002 "
       pdb="AL   ALF A1002 "
    ideal  model  delta    sigma   weight residual
    1.685  1.792 -0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" F1  ALF A1002 "
       pdb="AL   ALF A1002 "
    ideal  model  delta    sigma   weight residual
    1.684  1.787 -0.103 2.00e-02 2.50e+03 2.66e+01
  bond pdb=" F2  ALF A1002 "
       pdb="AL   ALF A1002 "
    ideal  model  delta    sigma   weight residual
    1.685  1.777 -0.092 2.00e-02 2.50e+03 2.13e+01
  bond pdb=" F4  ALF A1002 "
       pdb="AL   ALF A1002 "
    ideal  model  delta    sigma   weight residual
    1.686  1.766 -0.080 2.00e-02 2.50e+03 1.60e+01
  bond pdb=" C4  ADP A1001 "
       pdb=" C5  ADP A1001 "
    ideal  model  delta    sigma   weight residual
    1.490  1.454  0.036 2.00e-02 2.50e+03 3.26e+00
  ... (remaining 6952 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.19: 9420
       13.19 -    26.37: 4
       26.37 -    39.56: 0
       39.56 -    52.75: 0
       52.75 -    65.93: 2
  Bond angle restraints: 9426
  Sorted by residual:
  angle pdb=" F1  ALF A1002 "
        pdb="AL   ALF A1002 "
        pdb=" F2  ALF A1002 "
      ideal   model   delta    sigma   weight residual
     108.68  174.61  -65.93 3.00e+00 1.11e-01 4.83e+02
  angle pdb=" F3  ALF A1002 "
        pdb="AL   ALF A1002 "
        pdb=" F4  ALF A1002 "
      ideal   model   delta    sigma   weight residual
     109.63  175.41  -65.78 3.00e+00 1.11e-01 4.81e+02
  angle pdb=" F2  ALF A1002 "
        pdb="AL   ALF A1002 "
        pdb=" F4  ALF A1002 "
      ideal   model   delta    sigma   weight residual
     110.21   83.92   26.29 3.00e+00 1.11e-01 7.68e+01
  angle pdb=" F1  ALF A1002 "
        pdb="AL   ALF A1002 "
        pdb=" F4  ALF A1002 "
      ideal   model   delta    sigma   weight residual
     109.02   90.70   18.32 3.00e+00 1.11e-01 3.73e+01
  angle pdb=" F1  ALF A1002 "
        pdb="AL   ALF A1002 "
        pdb=" F3  ALF A1002 "
      ideal   model   delta    sigma   weight residual
     109.69   91.45   18.24 3.00e+00 1.11e-01 3.70e+01
  ... (remaining 9421 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.92: 3949
       21.92 -    43.84: 254
       43.84 -    65.77: 25
       65.77 -    87.69: 12
       87.69 -   109.61: 1
  Dihedral angle restraints: 4241
    sinusoidal: 1679
      harmonic: 2562
  Sorted by residual:
  dihedral pdb=" O2A ADP A1001 "
           pdb=" O3A ADP A1001 "
           pdb=" PA  ADP A1001 "
           pdb=" PB  ADP A1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -169.61  109.61     1      2.00e+01 2.50e-03 3.21e+01
  dihedral pdb=" CA  SER A 840 "
           pdb=" C   SER A 840 "
           pdb=" N   ASN A 841 "
           pdb=" CA  ASN A 841 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.94  -19.06     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CB  GLU A 374 "
           pdb=" CG  GLU A 374 "
           pdb=" CD  GLU A 374 "
           pdb=" OE1 GLU A 374 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.10  -85.10     1      3.00e+01 1.11e-03 9.76e+00
  ... (remaining 4238 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 942
       0.052 -    0.104: 166
       0.104 -    0.156: 22
       0.156 -    0.208: 0
       0.208 -    0.260: 1
  Chirality restraints: 1131
  Sorted by residual:
  chirality pdb=" C2' ADP A1001 "
            pdb=" C1' ADP A1001 "
            pdb=" C3' ADP A1001 "
            pdb=" O2' ADP A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.77    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CA  ASP A 180 "
            pdb=" N   ASP A 180 "
            pdb=" C   ASP A 180 "
            pdb=" CB  ASP A 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  LEU A 134 "
            pdb=" N   LEU A 134 "
            pdb=" C   LEU A 134 "
            pdb=" CB  LEU A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.22e-01
  ... (remaining 1128 not shown)

  Planarity restraints: 1186
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' ADP A1001 "    0.033 2.00e-02 2.50e+03   1.50e-02 6.17e+00
        pdb=" C2  ADP A1001 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4  ADP A1001 "   -0.011 2.00e-02 2.50e+03
        pdb=" C5  ADP A1001 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6  ADP A1001 "    0.019 2.00e-02 2.50e+03
        pdb=" C8  ADP A1001 "   -0.001 2.00e-02 2.50e+03
        pdb=" N1  ADP A1001 "    0.005 2.00e-02 2.50e+03
        pdb=" N3  ADP A1001 "   -0.016 2.00e-02 2.50e+03
        pdb=" N6  ADP A1001 "    0.011 2.00e-02 2.50e+03
        pdb=" N7  ADP A1001 "   -0.017 2.00e-02 2.50e+03
        pdb=" N9  ADP A1001 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 743 "    0.029 5.00e-02 4.00e+02   4.39e-02 3.09e+00
        pdb=" N   PRO A 744 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 744 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 744 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 135 "    0.021 5.00e-02 4.00e+02   3.24e-02 1.68e+00
        pdb=" N   PRO A 136 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 136 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 136 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1183 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1593
        2.79 -     3.31: 6725
        3.31 -     3.84: 11316
        3.84 -     4.37: 12548
        4.37 -     4.90: 21520
  Nonbonded interactions: 53702
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 417 "
            pdb=" OG1 THR A 420 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OD2 ASP A 172 "
            pdb=" OG  SER A 239 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" O   ILE A 306 "
            pdb="CA    CA A1000 "
     model   vdw
     2.303 2.510
  nonbonded pdb=" OG  SER A 186 "
            pdb=" O   GLU A 191 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" O   ARG A 468 "
            pdb=" NE2 GLN A 471 "
     model   vdw
     2.342 3.120
  ... (remaining 53697 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.590
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.107   6957  Z= 0.184
  Angle     :  1.221  65.934   9426  Z= 0.496
  Chirality :  0.039   0.260   1131
  Planarity :  0.004   0.044   1186
  Dihedral  : 14.519 109.609   2583
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.75 %
    Favored  : 97.12 %
  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: -1.69 (0.26), residues: 886
  helix: -0.27 (0.23), residues: 438
  sheet: -1.86 (0.46), residues: 118
  loop : -1.88 (0.31), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 842 
 TYR   0.005   0.001   TYR A 493 
 PHE   0.009   0.001   PHE A 176 
 TRP   0.004   0.000   TRP A 460 
 HIS   0.001   0.000   HIS A 624 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.18 ( 6957)
  covalent geometry    : angle       1.22125 /  0.50 ( 9426)
  hydrogen bonds       : bond        0.12863 /  9.25 (  377)
  hydrogen bonds       : angle       5.28723 /  3.75 ( 1137)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 248
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 MET cc_start: 0.3927 (mmm) cc_final: 0.3188 (mmp)
REVERT: A   81 ASN cc_start: 0.6219 (t0) cc_final: 0.5666 (m-40)
REVERT: A  110 ILE cc_start: 0.8752 (tt) cc_final: 0.8477 (tt)
REVERT: A  172 ASP cc_start: 0.7591 (m-30) cc_final: 0.7287 (m-30)
REVERT: A  355 LEU cc_start: 0.8674 (tp) cc_final: 0.7621 (tp)
REVERT: A  452 TYR cc_start: 0.6880 (m-80) cc_final: 0.6307 (m-80)
REVERT: A  510 TYR cc_start: 0.8759 (m-10) cc_final: 0.8448 (m-80)
REVERT: A  725 PHE cc_start: 0.3823 (m-80) cc_final: 0.3001 (m-80)
REVERT: A  834 PHE cc_start: 0.7042 (m-80) cc_final: 0.6567 (m-10)
REVERT: A  881 LEU cc_start: 0.8437 (mt) cc_final: 0.8028 (mp)
  outliers start: 1
  outliers final: 0
  residues processed: 249
  average time/residue: 0.0910
  time to fit residues: 29.1076
Evaluate side-chains
  150 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.2980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.2980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  43 GLN
A  61 ASN
A 120 GLN
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 202 GLN
A 249 GLN
A 458 GLN
A 592 GLN
** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 855 GLN
A 865 GLN
A 869 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.176695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.150048 restraints weight = 11673.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.150912 restraints weight = 8406.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.152655 restraints weight = 7135.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.152903 restraints weight = 4945.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.153134 restraints weight = 5086.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.3171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6957  Z= 0.141
  Angle     :  0.949  34.128   9426  Z= 0.402
  Chirality :  0.042   0.141   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.227  91.087    948
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 15.16 %
    Favored  : 81.96 %
  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: -0.31 (0.28), residues: 886
  helix:  0.97 (0.24), residues: 452
  sheet: -1.56 (0.54), residues: 90
  loop : -1.36 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 900 
 TYR   0.023   0.002   TYR A 618 
 PHE   0.017   0.001   PHE A 538 
 TRP   0.017   0.002   TRP A 795 
 HIS   0.003   0.001   HIS A  58 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.14 ( 6957)
  covalent geometry    : angle       0.94915 /  0.40 ( 9426)
  hydrogen bonds       : bond        0.03504 /  2.37 (  377)
  hydrogen bonds       : angle       3.84109 /  2.66 ( 1137)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 166
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 MET cc_start: 0.3991 (mmm) cc_final: 0.3760 (mmm)
REVERT: A   58 HIS cc_start: 0.6396 (m170) cc_final: 0.5945 (m170)
REVERT: A  110 ILE cc_start: 0.8499 (tt) cc_final: 0.8228 (tt)
REVERT: A  452 TYR cc_start: 0.7047 (m-80) cc_final: 0.6422 (m-80)
REVERT: A  510 TYR cc_start: 0.8959 (m-10) cc_final: 0.8597 (m-80)
REVERT: A  511 GLN cc_start: 0.7869 (tm-30) cc_final: 0.7612 (tp40)
REVERT: A  568 MET cc_start: 0.8259 (tpt) cc_final: 0.7201 (tpt)
REVERT: A  784 ILE cc_start: 0.9018 (tp) cc_final: 0.8803 (tp)
REVERT: A  834 PHE cc_start: 0.7132 (m-80) cc_final: 0.6884 (m-10)
REVERT: A  868 PHE cc_start: 0.6594 (OUTLIER) cc_final: 0.5039 (t80)
REVERT: A  881 LEU cc_start: 0.8279 (mt) cc_final: 0.8026 (mp)
REVERT: A  901 SER cc_start: 0.8860 (m) cc_final: 0.8509 (t)
  outliers start: 22
  outliers final: 17
  residues processed: 179
  average time/residue: 0.0802
  time to fit residues: 19.0841
Evaluate side-chains
  155 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  249 GLN
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  396 PHE
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  602 MET
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  842 ARG
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  855 GLN
Chi-restraints excluded: chain A residue  868 PHE
Chi-restraints excluded: chain A residue  876 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 61 optimal weight:    0.0970
   chunk 35 optimal weight:    0.8980
   chunk 23 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 82 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0970
   chunk 4 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5376

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 249 GLN
** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 855 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.170677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.141321 restraints weight = 11506.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.143008 restraints weight = 8351.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.144591 restraints weight = 6242.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.145082 restraints weight = 4733.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.145336 restraints weight = 4608.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.3784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6957  Z= 0.129
  Angle     :  0.928  29.461   9426  Z= 0.387
  Chirality :  0.041   0.144   1131
  Planarity :  0.004   0.049   1186
  Dihedral  :  5.211  91.030    948
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.91 %
    Favored  : 78.69 %
  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:  0.12 (0.29), residues: 886
  helix:  1.42 (0.24), residues: 448
  sheet: -1.45 (0.49), residues: 118
  loop : -1.20 (0.36), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 153 
 TYR   0.017   0.001   TYR A 618 
 PHE   0.012   0.001   PHE A  63 
 TRP   0.018   0.001   TRP A 795 
 HIS   0.006   0.001   HIS A  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 ( 6957)
  covalent geometry    : angle       0.92839 /  0.39 ( 9426)
  hydrogen bonds       : bond        0.03430 /  2.30 (  377)
  hydrogen bonds       : angle       3.72806 /  2.58 ( 1137)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 163
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLU cc_start: 0.5376 (pt0) cc_final: 0.5126 (pt0)
REVERT: A  213 ARG cc_start: 0.6145 (mtp180) cc_final: 0.5942 (mmm160)
REVERT: A  901 SER cc_start: 0.8882 (m) cc_final: 0.8551 (t)
  outliers start: 26
  outliers final: 17
  residues processed: 175
  average time/residue: 0.0717
  time to fit residues: 16.7778
Evaluate side-chains
  160 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  249 GLN
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  396 PHE
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  842 ARG
Chi-restraints excluded: chain A residue  856 LEU
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  876 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 88 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 21 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  61 ASN
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 249 GLN
A 364 HIS
A 494 GLN
A 730 ASN
** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 855 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.165039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.134867 restraints weight = 11533.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.136751 restraints weight = 7822.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.138198 restraints weight = 5807.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.138209 restraints weight = 5353.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.138724 restraints weight = 4632.268|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.4510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6957  Z= 0.153
  Angle     :  0.934  29.798   9426  Z= 0.394
  Chirality :  0.041   0.149   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.322  92.340    948
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 20.92 %
    Favored  : 75.03 %
  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:  0.38 (0.30), residues: 886
  helix:  1.61 (0.25), residues: 461
  sheet: -1.80 (0.51), residues: 107
  loop : -0.99 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 153 
 TYR   0.015   0.001   TYR A 618 
 PHE   0.017   0.002   PHE A 245 
 TRP   0.018   0.002   TRP A 795 
 HIS   0.007   0.001   HIS A  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.15 ( 6957)
  covalent geometry    : angle       0.93359 /  0.39 ( 9426)
  hydrogen bonds       : bond        0.03739 /  2.51 (  377)
  hydrogen bonds       : angle       3.68500 /  2.56 ( 1137)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 157
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  435 MET cc_start: 0.7470 (ptt) cc_final: 0.7158 (ptt)
REVERT: A  442 LEU cc_start: 0.7982 (mm) cc_final: 0.7480 (tp)
REVERT: A  568 MET cc_start: 0.8333 (tpt) cc_final: 0.7298 (tpt)
REVERT: A  881 LEU cc_start: 0.8351 (mp) cc_final: 0.8025 (mp)
REVERT: A  901 SER cc_start: 0.8918 (m) cc_final: 0.8588 (t)
  outliers start: 31
  outliers final: 23
  residues processed: 174
  average time/residue: 0.0713
  time to fit residues: 16.9322
Evaluate side-chains
  156 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  249 GLN
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  396 PHE
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  842 ARG
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  855 GLN
Chi-restraints excluded: chain A residue  856 LEU
Chi-restraints excluded: chain A residue  873 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 69 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 38 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 149 HIS
** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 855 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.163267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.132778 restraints weight = 11680.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.133789 restraints weight = 8185.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.136136 restraints weight = 6233.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.136218 restraints weight = 4766.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.136625 restraints weight = 4642.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.4844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6957  Z= 0.142
  Angle     :  0.936  29.579   9426  Z= 0.392
  Chirality :  0.041   0.148   1131
  Planarity :  0.004   0.046   1186
  Dihedral  :  5.336  90.975    948
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 23.92 %
    Favored  : 72.55 %
  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:  0.46 (0.30), residues: 886
  helix:  1.68 (0.25), residues: 461
  sheet: -1.72 (0.52), residues: 107
  loop : -0.97 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 827 
 TYR   0.013   0.001   TYR A 618 
 PHE   0.009   0.001   PHE A 702 
 TRP   0.032   0.002   TRP A  72 
 HIS   0.013   0.002   HIS A  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00332 /  0.14 ( 6957)
  covalent geometry    : angle       0.93628 /  0.39 ( 9426)
  hydrogen bonds       : bond        0.03648 /  2.46 (  377)
  hydrogen bonds       : angle       3.65859 /  2.55 ( 1137)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 154
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 PHE cc_start: 0.6677 (m-80) cc_final: 0.6284 (m-80)
REVERT: A  435 MET cc_start: 0.7577 (ptt) cc_final: 0.7334 (ptt)
REVERT: A  442 LEU cc_start: 0.7925 (mm) cc_final: 0.7526 (tp)
REVERT: A  568 MET cc_start: 0.8386 (tpt) cc_final: 0.7484 (tpt)
REVERT: A  901 SER cc_start: 0.8954 (m) cc_final: 0.8635 (t)
  outliers start: 27
  outliers final: 17
  residues processed: 170
  average time/residue: 0.0753
  time to fit residues: 17.4960
Evaluate side-chains
  156 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  856 LEU
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  873 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 44 optimal weight:    0.6980
   chunk 58 optimal weight:    0.4980
   chunk 20 optimal weight:    0.4980
   chunk 26 optimal weight:    0.0060
   chunk 82 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   chunk 60 optimal weight:    0.0020
   chunk 71 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.3204

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  61 ASN
** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.168586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.139286 restraints weight = 11577.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.141725 restraints weight = 7397.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.142942 restraints weight = 5338.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.142774 restraints weight = 5036.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.143094 restraints weight = 4566.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6957  Z= 0.117
  Angle     :  0.932  29.596   9426  Z= 0.389
  Chirality :  0.041   0.147   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.202  88.146    948
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 24.97 %
    Favored  : 72.03 %
  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:  0.63 (0.30), residues: 886
  helix:  1.77 (0.25), residues: 460
  sheet: -1.50 (0.55), residues: 97
  loop : -0.90 (0.37), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 153 
 TYR   0.014   0.001   TYR A 618 
 PHE   0.012   0.001   PHE A 454 
 TRP   0.037   0.002   TRP A  72 
 HIS   0.012   0.002   HIS A  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 6957)
  covalent geometry    : angle       0.93241 /  0.39 ( 9426)
  hydrogen bonds       : bond        0.03314 /  2.23 (  377)
  hydrogen bonds       : angle       3.62408 /  2.52 ( 1137)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 150
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 PHE cc_start: 0.6585 (m-80) cc_final: 0.6260 (m-80)
REVERT: A  431 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8492 (mt)
REVERT: A  442 LEU cc_start: 0.7934 (mm) cc_final: 0.7596 (tp)
REVERT: A  568 MET cc_start: 0.8327 (tpt) cc_final: 0.7564 (tpt)
REVERT: A  587 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.6881 (m-80)
REVERT: A  630 LYS cc_start: 0.8421 (mmmt) cc_final: 0.7691 (mtpt)
REVERT: A  901 SER cc_start: 0.8944 (m) cc_final: 0.8638 (t)
  outliers start: 23
  outliers final: 16
  residues processed: 162
  average time/residue: 0.0722
  time to fit residues: 16.2742
Evaluate side-chains
  155 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  431 ILE
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  856 LEU
Chi-restraints excluded: chain A residue  873 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 86 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 80 optimal weight:    0.3980
   chunk 16 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 249 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 = 0.4070 r_free = 0.4070 target = 0.162931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.132415 restraints weight = 11596.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.133318 restraints weight = 7947.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.134211 restraints weight = 6338.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.134495 restraints weight = 5899.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.136950 restraints weight = 5179.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.5354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6957  Z= 0.154
  Angle     :  0.961  29.498   9426  Z= 0.406
  Chirality :  0.042   0.159   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.364  88.941    948
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 24.58 %
    Favored  : 71.50 %
  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:  0.52 (0.30), residues: 886
  helix:  1.69 (0.25), residues: 461
  sheet: -1.77 (0.51), residues: 107
  loop : -0.85 (0.38), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 827 
 TYR   0.012   0.001   TYR A 618 
 PHE   0.011   0.001   PHE A 245 
 TRP   0.034   0.002   TRP A  72 
 HIS   0.011   0.002   HIS A  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.15 ( 6957)
  covalent geometry    : angle       0.96126 /  0.41 ( 9426)
  hydrogen bonds       : bond        0.03799 /  2.55 (  377)
  hydrogen bonds       : angle       3.77616 /  2.63 ( 1137)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 148
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.7180 (m-10) cc_final: 0.6846 (m-80)
REVERT: A  218 PHE cc_start: 0.6677 (m-80) cc_final: 0.6335 (m-80)
REVERT: A  264 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8471 (tt)
REVERT: A  435 MET cc_start: 0.7155 (ptt) cc_final: 0.6838 (ptt)
REVERT: A  442 LEU cc_start: 0.7938 (mm) cc_final: 0.7586 (tp)
REVERT: A  630 LYS cc_start: 0.8474 (mmmt) cc_final: 0.7802 (mtpt)
REVERT: A  732 MET cc_start: 0.8058 (mmm) cc_final: 0.7844 (mmt)
REVERT: A  901 SER cc_start: 0.9025 (m) cc_final: 0.8713 (t)
  outliers start: 30
  outliers final: 24
  residues processed: 165
  average time/residue: 0.0738
  time to fit residues: 16.6019
Evaluate side-chains
  164 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 139
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  583 ARG
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  807 ASP
Chi-restraints excluded: chain A residue  856 LEU
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  873 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 46 optimal weight:    0.2980
   chunk 44 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  61 ASN
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 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 = 0.4013 r_free = 0.4013 target = 0.158198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.125004 restraints weight = 11725.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.126352 restraints weight = 7724.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.127173 restraints weight = 6267.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.127383 restraints weight = 5491.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.129011 restraints weight = 5197.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.5512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6957  Z= 0.145
  Angle     :  0.967  29.604   9426  Z= 0.411
  Chirality :  0.043   0.163   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.369  87.735    948
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 26.41 %
    Favored  : 69.67 %
  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:  0.62 (0.30), residues: 886
  helix:  1.73 (0.25), residues: 461
  sheet: -1.57 (0.54), residues: 97
  loop : -0.83 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 760 
 TYR   0.013   0.001   TYR A 397 
 PHE   0.010   0.001   PHE A 702 
 TRP   0.036   0.002   TRP A  72 
 HIS   0.008   0.001   HIS A  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.14 ( 6957)
  covalent geometry    : angle       0.96654 /  0.41 ( 9426)
  hydrogen bonds       : bond        0.03724 /  2.51 (  377)
  hydrogen bonds       : angle       3.74645 /  2.60 ( 1137)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 LEU cc_start: 0.7594 (tp) cc_final: 0.7375 (tp)
REVERT: A  218 PHE cc_start: 0.6745 (m-80) cc_final: 0.6368 (m-80)
REVERT: A  442 LEU cc_start: 0.7970 (mm) cc_final: 0.7685 (tp)
REVERT: A  447 ILE cc_start: 0.7688 (mm) cc_final: 0.7449 (mp)
REVERT: A  630 LYS cc_start: 0.8509 (mmmt) cc_final: 0.7886 (mtpt)
REVERT: A  732 MET cc_start: 0.8043 (mmm) cc_final: 0.7830 (mmt)
REVERT: A  901 SER cc_start: 0.9041 (m) cc_final: 0.8719 (t)
  outliers start: 30
  outliers final: 26
  residues processed: 161
  average time/residue: 0.0750
  time to fit residues: 16.5752
Evaluate side-chains
  169 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  583 ARG
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  845 CYS
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  856 LEU
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0670
   chunk 29 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.6718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  61 ASN
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 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 = 0.3995 r_free = 0.3995 target = 0.156221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.125115 restraints weight = 11711.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.126363 restraints weight = 7584.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.127151 restraints weight = 5960.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.127393 restraints weight = 5408.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.127802 restraints weight = 5137.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.5668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6957  Z= 0.143
  Angle     :  0.980  29.633   9426  Z= 0.416
  Chirality :  0.043   0.182   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.389  86.085    948
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 26.41 %
    Favored  : 69.41 %
  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:  0.59 (0.30), residues: 886
  helix:  1.74 (0.25), residues: 461
  sheet: -1.58 (0.54), residues: 97
  loop : -0.89 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 468 
 TYR   0.013   0.001   TYR A 397 
 PHE   0.019   0.001   PHE A 861 
 TRP   0.036   0.002   TRP A  72 
 HIS   0.009   0.001   HIS A  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 ( 6957)
  covalent geometry    : angle       0.98024 /  0.42 ( 9426)
  hydrogen bonds       : bond        0.03723 /  2.52 (  377)
  hydrogen bonds       : angle       3.75358 /  2.62 ( 1137)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 147
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 LEU cc_start: 0.7901 (mm) cc_final: 0.7460 (mp)
REVERT: A  218 PHE cc_start: 0.6643 (m-80) cc_final: 0.6308 (m-80)
REVERT: A  442 LEU cc_start: 0.8046 (mm) cc_final: 0.7768 (tp)
REVERT: A  630 LYS cc_start: 0.8498 (mmmt) cc_final: 0.7896 (mtpt)
REVERT: A  732 MET cc_start: 0.8026 (mmm) cc_final: 0.7820 (mmt)
REVERT: A  901 SER cc_start: 0.9034 (m) cc_final: 0.8804 (t)
  outliers start: 32
  outliers final: 25
  residues processed: 164
  average time/residue: 0.0739
  time to fit residues: 16.4103
Evaluate side-chains
  166 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 141
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  583 ARG
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  856 LEU
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0970
   chunk 47 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0050
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.5192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  61 ASN
** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.156753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.122937 restraints weight = 11587.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.126295 restraints weight = 7105.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.128373 restraints weight = 5184.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.130013 restraints weight = 4246.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.130816 restraints weight = 3679.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.5745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6957  Z= 0.135
  Angle     :  0.994  29.639   9426  Z= 0.424
  Chirality :  0.043   0.188   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.377  84.485    948
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 27.58 %
    Favored  : 69.02 %
  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:  0.61 (0.30), residues: 886
  helix:  1.75 (0.25), residues: 461
  sheet: -1.55 (0.54), residues: 97
  loop : -0.88 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 473 
 TYR   0.014   0.001   TYR A 397 
 PHE   0.018   0.001   PHE A 861 
 TRP   0.036   0.002   TRP A  72 
 HIS   0.010   0.001   HIS A  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.13 ( 6957)
  covalent geometry    : angle       0.99379 /  0.42 ( 9426)
  hydrogen bonds       : bond        0.03637 /  2.44 (  377)
  hydrogen bonds       : angle       3.76112 /  2.62 ( 1137)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  175 LEU cc_start: 0.7981 (mm) cc_final: 0.7504 (mp)
REVERT: A  218 PHE cc_start: 0.6725 (m-80) cc_final: 0.6347 (m-80)
REVERT: A  274 PHE cc_start: 0.8484 (m-10) cc_final: 0.8229 (m-80)
REVERT: A  293 GLU cc_start: 0.7325 (pp20) cc_final: 0.7067 (pp20)
REVERT: A  442 LEU cc_start: 0.8006 (mm) cc_final: 0.7792 (tp)
REVERT: A  587 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.6756 (m-80)
REVERT: A  630 LYS cc_start: 0.8467 (mmmt) cc_final: 0.7852 (mtpt)
REVERT: A  631 SER cc_start: 0.8900 (t) cc_final: 0.8483 (p)
REVERT: A  732 MET cc_start: 0.8110 (mmm) cc_final: 0.7903 (mmt)
REVERT: A  757 ASP cc_start: 0.6526 (m-30) cc_final: 0.6319 (m-30)
  outliers start: 26
  outliers final: 24
  residues processed: 162
  average time/residue: 0.0699
  time to fit residues: 15.6002
Evaluate side-chains
  168 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 143
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  418 ASN
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  583 ARG
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  856 LEU
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 75 optimal weight:    0.2980
   chunk 41 optimal weight:    0.3980
   chunk 81 optimal weight:    1.9990
   chunk 78 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0970
   chunk 71 optimal weight:    0.3980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.3178

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  61 ASN
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.160048 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.128627 restraints weight = 11516.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.130119 restraints weight = 7196.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.130563 restraints weight = 5654.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.131105 restraints weight = 5403.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.131367 restraints weight = 4902.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.5730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6957  Z= 0.125
  Angle     :  0.987  29.645   9426  Z= 0.418
  Chirality :  0.043   0.166   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.296  82.911    948
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 28.63 %
    Favored  : 68.24 %
  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:  0.67 (0.30), residues: 886
  helix:  1.78 (0.25), residues: 461
  sheet: -1.50 (0.55), residues: 97
  loop : -0.83 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 468 
 TYR   0.015   0.001   TYR A 397 
 PHE   0.016   0.001   PHE A 861 
 TRP   0.033   0.002   TRP A  72 
 HIS   0.010   0.001   HIS A  98 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 ( 6957)
  covalent geometry    : angle       0.98691 /  0.42 ( 9426)
  hydrogen bonds       : bond        0.03439 /  2.31 (  377)
  hydrogen bonds       : angle       3.69607 /  2.59 ( 1137)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1269.16 seconds
wall clock time: 22 minutes 40.59 seconds (1360.59 seconds total)