Starting phenix.real_space_refine
on Fri Aug 22 18:52:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iww_35781/08_2025/8iww_35781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iww_35781/08_2025/8iww_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iww_35781/08_2025/8iww_35781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iww_35781/08_2025/8iww_35781.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iww_35781/08_2025/8iww_35781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iww_35781/08_2025/8iww_35781.map"
  }
  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-2.0-5787/lib/python3.9/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: 1.45, per 1000 atoms: 0.21
  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: 0.47
  Conformation dependent library (CDL) restraints added in 379.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.28
  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: 1.19

  Time building geometry restraints manager: 0.67 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:             3.580
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.490
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
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 aren 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
  covalent geometry    : bond        0.00336 ( 6957)
  covalent geometry    : angle       1.22125 ( 9426)
  hydrogen bonds       : bond        0.12863 (  377)
  hydrogen bonds       : angle       5.28723 ( 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  : 0.261 
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: 0.3187 (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: 0.7288 (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: 0.3000 (m-80)
REVERT: A  834 PHE cc_start: 0.7042 (m-80) cc_final: 0.6567 (m-10)
REVERT: A  881 LEU cc_start: 0.8436 (mt) cc_final: 0.8029 (mp)
  outliers start: 1
  outliers final: 0
  residues processed: 249
  average time/residue: 0.0925
  time to fit residues: 29.2734
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  : 0.169 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4230 r_free = 0.4230 target = 0.177272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.149590 restraints weight = 11689.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.149581 restraints weight = 8356.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.151880 restraints weight = 7026.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.152238 restraints weight = 5307.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.152667 restraints weight = 5017.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6957  Z= 0.141
  Angle     :  0.947  33.569   9426  Z= 0.401
  Chirality :  0.042   0.134   1131
  Planarity :  0.004   0.044   1186
  Dihedral  :  5.247  92.336    948
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 14.38 %
    Favored  : 82.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.28), residues: 886
  helix:  0.97 (0.24), residues: 452
  sheet: -1.12 (0.53), residues: 101
  loop : -1.45 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 403 
 TYR   0.022   0.002   TYR A 618 
 PHE   0.016   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
  covalent geometry    : bond        0.00321 ( 6957)
  covalent geometry    : angle       0.94736 ( 9426)
  hydrogen bonds       : bond        0.03522 (  377)
  hydrogen bonds       : angle       3.85461 ( 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
  189 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 166
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 MET cc_start: 0.3801 (mmm) cc_final: 0.3581 (mmm)
REVERT: A   81 ASN cc_start: 0.5924 (t0) cc_final: 0.5678 (m-40)
REVERT: A  110 ILE cc_start: 0.8637 (tt) cc_final: 0.8380 (tt)
REVERT: A  172 ASP cc_start: 0.7901 (m-30) cc_final: 0.7696 (m-30)
REVERT: A  452 TYR cc_start: 0.7050 (m-80) cc_final: 0.6457 (m-80)
REVERT: A  510 TYR cc_start: 0.8956 (m-10) cc_final: 0.8595 (m-80)
REVERT: A  568 MET cc_start: 0.8225 (tpt) cc_final: 0.6890 (tpt)
REVERT: A  784 ILE cc_start: 0.9012 (tp) cc_final: 0.8799 (tp)
REVERT: A  834 PHE cc_start: 0.7148 (m-80) cc_final: 0.6877 (m-10)
REVERT: A  868 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.5112 (t80)
REVERT: A  881 LEU cc_start: 0.8259 (mt) cc_final: 0.8010 (mp)
  outliers start: 23
  outliers final: 17
  residues processed: 180
  average time/residue: 0.0760
  time to fit residues: 18.0848
Evaluate side-chains
  154 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 136
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 35 optimal weight:    0.0970
   chunk 23 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 249 GLN
A 730 ASN
** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 855 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.166435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.133257 restraints weight = 11474.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.134280 restraints weight = 8206.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.136107 restraints weight = 6487.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.136443 restraints weight = 5163.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.136783 restraints weight = 4861.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.4299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6957  Z= 0.194
  Angle     :  0.969  30.002   9426  Z= 0.416
  Chirality :  0.043   0.147   1131
  Planarity :  0.005   0.045   1186
  Dihedral  :  5.432  94.761    948
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 17.65 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.00 (0.29), residues: 886
  helix:  1.26 (0.24), residues: 454
  sheet: -1.83 (0.50), residues: 105
  loop : -1.09 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 468 
 TYR   0.016   0.002   TYR A 618 
 PHE   0.010   0.002   PHE A 617 
 TRP   0.019   0.002   TRP A 795 
 HIS   0.009   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 6957)
  covalent geometry    : angle       0.96943 ( 9426)
  hydrogen bonds       : bond        0.04191 (  377)
  hydrogen bonds       : angle       3.94364 ( 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
  196 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 161
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6308 (t0) cc_final: 0.6003 (m-40)
REVERT: A  100 PHE cc_start: 0.7492 (m-10) cc_final: 0.7130 (m-80)
REVERT: A  172 ASP cc_start: 0.8164 (m-30) cc_final: 0.7872 (m-30)
REVERT: A  901 SER cc_start: 0.8893 (m) cc_final: 0.8608 (t)
  outliers start: 35
  outliers final: 24
  residues processed: 180
  average time/residue: 0.0637
  time to fit residues: 15.3654
Evaluate side-chains
  164 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  161 VAL
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  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  707 LEU
Chi-restraints excluded: chain A residue  842 ARG
Chi-restraints excluded: chain A residue  852 ILE
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:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    9.9990
   chunk 88 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0980
   chunk 21 optimal weight:    0.0050
   chunk 15 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 149 HIS
A 249 GLN
A 364 HIS
A 494 GLN
** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.161408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.130324 restraints weight = 11695.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.131376 restraints weight = 8038.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.133075 restraints weight = 6346.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.133554 restraints weight = 4960.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.134022 restraints weight = 4632.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.4523

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= 0.122
  Angle     :  0.926  29.629   9426  Z= 0.385
  Chirality :  0.041   0.146   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.290  91.729    948
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 22.22 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.30), residues: 886
  helix:  1.57 (0.25), residues: 461
  sheet: -1.20 (0.52), residues: 106
  loop : -1.16 (0.37), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 900 
 TYR   0.016   0.001   TYR A 618 
 PHE   0.009   0.001   PHE A 538 
 TRP   0.020   0.001   TRP A 795 
 HIS   0.013   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6957)
  covalent geometry    : angle       0.92599 ( 9426)
  hydrogen bonds       : bond        0.03538 (  377)
  hydrogen bonds       : angle       3.70680 ( 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
  181 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 157
  time to evaluate  : 0.271 
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  100 PHE cc_start: 0.7176 (m-10) cc_final: 0.6919 (m-80)
REVERT: A  172 ASP cc_start: 0.7982 (m-30) cc_final: 0.7744 (m-30)
REVERT: A  442 LEU cc_start: 0.7956 (mm) cc_final: 0.7466 (tp)
REVERT: A  568 MET cc_start: 0.8238 (tpt) cc_final: 0.7439 (tpt)
REVERT: A  901 SER cc_start: 0.8923 (m) cc_final: 0.8708 (t)
  outliers start: 24
  outliers final: 18
  residues processed: 172
  average time/residue: 0.0627
  time to fit residues: 15.0382
Evaluate side-chains
  164 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
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  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  600 ASP
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  852 ILE
Chi-restraints excluded: chain A residue  856 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 69 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 43 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
A 140 HIS
** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 855 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.158731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.127667 restraints weight = 11854.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.129154 restraints weight = 8480.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.130237 restraints weight = 6999.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.130503 restraints weight = 5448.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.130904 restraints weight = 5076.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.4872

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= 0.151
  Angle     :  0.937  29.723   9426  Z= 0.391
  Chirality :  0.041   0.152   1131
  Planarity :  0.004   0.046   1186
  Dihedral  :  5.362  92.167    948
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 23.40 %
    Favored  : 72.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.30), residues: 886
  helix:  1.55 (0.25), residues: 466
  sheet: -1.82 (0.51), residues: 107
  loop : -0.88 (0.38), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 900 
 TYR   0.014   0.001   TYR A 618 
 PHE   0.008   0.001   PHE A 702 
 TRP   0.032   0.002   TRP A  72 
 HIS   0.012   0.002   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 6957)
  covalent geometry    : angle       0.93673 ( 9426)
  hydrogen bonds       : bond        0.03717 (  377)
  hydrogen bonds       : angle       3.73647 ( 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
  187 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 157
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.7229 (m-10) cc_final: 0.6921 (m-80)
REVERT: A  172 ASP cc_start: 0.8080 (m-30) cc_final: 0.7832 (m-30)
REVERT: A  442 LEU cc_start: 0.7959 (mm) cc_final: 0.7491 (tp)
REVERT: A  901 SER cc_start: 0.8950 (m) cc_final: 0.8639 (t)
  outliers start: 30
  outliers final: 23
  residues processed: 173
  average time/residue: 0.0705
  time to fit residues: 16.7135
Evaluate side-chains
  163 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
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  396 PHE
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  707 LEU
Chi-restraints excluded: chain A residue  741 MET
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0010
   chunk 71 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0970
   chunk 55 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
A 855 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.159061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.127565 restraints weight = 11839.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.128948 restraints weight = 7743.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.129726 restraints weight = 6045.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.129964 restraints weight = 5643.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.132861 restraints weight = 4960.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.5106

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= 0.127
  Angle     :  0.933  29.551   9426  Z= 0.390
  Chirality :  0.041   0.156   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.259  89.837    948
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 24.44 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.30), residues: 886
  helix:  1.66 (0.25), residues: 466
  sheet: -1.61 (0.54), residues: 97
  loop : -0.84 (0.38), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 900 
 TYR   0.014   0.001   TYR A 618 
 PHE   0.016   0.001   PHE A 245 
 TRP   0.035   0.002   TRP A  72 
 HIS   0.010   0.002   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6957)
  covalent geometry    : angle       0.93322 ( 9426)
  hydrogen bonds       : bond        0.03498 (  377)
  hydrogen bonds       : angle       3.67052 ( 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
  170 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 PHE cc_start: 0.7246 (m-10) cc_final: 0.6890 (m-80)
REVERT: A  172 ASP cc_start: 0.8201 (m-30) cc_final: 0.7885 (m-30)
REVERT: A  218 PHE cc_start: 0.6937 (m-80) cc_final: 0.6478 (m-80)
REVERT: A  219 MET cc_start: 0.8265 (tmm) cc_final: 0.8064 (ppp)
REVERT: A  281 MET cc_start: 0.7237 (tpt) cc_final: 0.7000 (tpt)
REVERT: A  442 LEU cc_start: 0.7918 (mm) cc_final: 0.7508 (tp)
REVERT: A  568 MET cc_start: 0.8277 (tpt) cc_final: 0.7683 (tpt)
REVERT: A  671 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7394 (tm-30)
REVERT: A  732 MET cc_start: 0.8004 (mmm) cc_final: 0.7783 (mmt)
REVERT: A  881 LEU cc_start: 0.8471 (mt) cc_final: 0.8271 (mp)
REVERT: A  901 SER cc_start: 0.8978 (m) cc_final: 0.8664 (t)
  outliers start: 24
  outliers final: 19
  residues processed: 159
  average time/residue: 0.0718
  time to fit residues: 15.7672
Evaluate side-chains
  157 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 138
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  162 CYS
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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    0.2980
   chunk 48 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
A 855 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.155831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.123798 restraints weight = 11631.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.125048 restraints weight = 7294.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.125537 restraints weight = 5659.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.125867 restraints weight = 5398.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.126296 restraints weight = 4955.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.5507

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= 0.146
  Angle     :  0.955  29.587   9426  Z= 0.399
  Chirality :  0.042   0.162   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.383  89.575    948
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 23.92 %
    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 aren not related in a simple way.
  whole:  0.53 (0.30), residues: 886
  helix:  1.62 (0.25), residues: 467
  sheet: -1.65 (0.54), residues: 97
  loop : -0.84 (0.38), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 153 
 TYR   0.012   0.001   TYR A 618 
 PHE   0.018   0.001   PHE A 245 
 TRP   0.036   0.002   TRP A  72 
 HIS   0.011   0.002   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6957)
  covalent geometry    : angle       0.95468 ( 9426)
  hydrogen bonds       : bond        0.03776 (  377)
  hydrogen bonds       : angle       3.71997 ( 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
  187 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 152
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 ASP cc_start: 0.8146 (m-30) cc_final: 0.7850 (m-30)
REVERT: A  218 PHE cc_start: 0.6810 (m-80) cc_final: 0.6408 (m-80)
REVERT: A  442 LEU cc_start: 0.8039 (mm) cc_final: 0.7638 (tp)
REVERT: A  568 MET cc_start: 0.8360 (tpt) cc_final: 0.7831 (tpt)
REVERT: A  901 SER cc_start: 0.9039 (m) cc_final: 0.8728 (t)
  outliers start: 35
  outliers final: 25
  residues processed: 175
  average time/residue: 0.0735
  time to fit residues: 17.8835
Evaluate side-chains
  173 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 148
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 ILE
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  264 LEU
Chi-restraints excluded: chain A residue  354 THR
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  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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 35 optimal weight:    4.9990
   chunk 82 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0770
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 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 = 0.3993 r_free = 0.3993 target = 0.156203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.125704 restraints weight = 11681.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.126795 restraints weight = 8421.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.127831 restraints weight = 6545.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.128008 restraints weight = 5863.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.129474 restraints weight = 5148.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.5642

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= 0.144
  Angle     :  0.960  29.629   9426  Z= 0.406
  Chirality :  0.042   0.145   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.357  88.310    948
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 25.10 %
    Favored  : 70.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.30), residues: 886
  helix:  1.69 (0.25), residues: 467
  sheet: -1.53 (0.54), residues: 97
  loop : -0.86 (0.38), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 153 
 TYR   0.014   0.001   TYR A 618 
 PHE   0.010   0.001   PHE A 454 
 TRP   0.036   0.002   TRP A  72 
 HIS   0.006   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6957)
  covalent geometry    : angle       0.96020 ( 9426)
  hydrogen bonds       : bond        0.03735 (  377)
  hydrogen bonds       : angle       3.66740 ( 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
  187 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 153
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 ASP cc_start: 0.8112 (m-30) cc_final: 0.7837 (m-30)
REVERT: A  218 PHE cc_start: 0.6693 (m-80) cc_final: 0.6348 (m-80)
REVERT: A  247 MET cc_start: 0.8097 (tpt) cc_final: 0.7880 (mmt)
REVERT: A  442 LEU cc_start: 0.8028 (mm) cc_final: 0.7603 (tp)
REVERT: A  568 MET cc_start: 0.8322 (tpt) cc_final: 0.7894 (tpt)
REVERT: A  901 SER cc_start: 0.9068 (m) cc_final: 0.8761 (t)
  outliers start: 34
  outliers final: 29
  residues processed: 172
  average time/residue: 0.0565
  time to fit residues: 13.9725
Evaluate side-chains
  167 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
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  231 VAL
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  354 THR
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  580 ILE
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  807 ASP
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:    0.6980
   chunk 73 optimal weight:    0.1980
   chunk 74 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0020
   chunk 81 optimal weight:    0.1980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.3588

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
A 120 GLN
A 418 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.160003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.128207 restraints weight = 11756.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.129071 restraints weight = 7500.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.129513 restraints weight = 6154.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.130016 restraints weight = 5883.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.130804 restraints weight = 5284.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.5660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6957  Z= 0.125
  Angle     :  0.961  29.659   9426  Z= 0.405
  Chirality :  0.042   0.160   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.216  84.770    948
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 26.41 %
    Favored  : 69.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.30), residues: 886
  helix:  1.80 (0.25), residues: 461
  sheet: -1.28 (0.58), residues: 91
  loop : -0.77 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 153 
 TYR   0.013   0.001   TYR A 618 
 PHE   0.010   0.001   PHE A 454 
 TRP   0.033   0.002   TRP A 795 
 HIS   0.008   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6957)
  covalent geometry    : angle       0.96135 ( 9426)
  hydrogen bonds       : bond        0.03411 (  377)
  hydrogen bonds       : angle       3.58268 ( 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
  177 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A  172 ASP cc_start: 0.8160 (m-30) cc_final: 0.7841 (m-30)
REVERT: A  218 PHE cc_start: 0.6668 (m-80) cc_final: 0.6286 (m-10)
REVERT: A  281 MET cc_start: 0.7344 (tpt) cc_final: 0.7021 (tpt)
REVERT: A  442 LEU cc_start: 0.7959 (mm) cc_final: 0.7569 (tp)
REVERT: A  568 MET cc_start: 0.8307 (tpt) cc_final: 0.7901 (tpt)
REVERT: A  587 TYR cc_start: 0.8005 (OUTLIER) cc_final: 0.6881 (m-80)
REVERT: A  661 MET cc_start: 0.8274 (mmm) cc_final: 0.7883 (mmm)
REVERT: A  901 SER cc_start: 0.9068 (m) cc_final: 0.8781 (t)
  outliers start: 28
  outliers final: 23
  residues processed: 167
  average time/residue: 0.0663
  time to fit residues: 15.3192
Evaluate side-chains
  164 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 140
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 THR
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  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  580 ILE
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 29 optimal weight:    0.0470
   chunk 30 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 11 optimal weight:    3.9990
   chunk 82 optimal weight:    0.1980
   chunk 58 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0770
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
A 418 ASN
A 467 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.159542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.129647 restraints weight = 11577.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.131291 restraints weight = 7850.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.132257 restraints weight = 5798.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.132529 restraints weight = 5030.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.132845 restraints weight = 4716.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.5801

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= 0.132
  Angle     :  0.980  29.654   9426  Z= 0.415
  Chirality :  0.042   0.159   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.224  83.640    948
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 26.54 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.30), residues: 886
  helix:  1.70 (0.25), residues: 461
  sheet: -1.27 (0.58), residues: 91
  loop : -0.74 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 153 
 TYR   0.013   0.001   TYR A 618 
 PHE   0.012   0.001   PHE A  63 
 TRP   0.032   0.002   TRP A 795 
 HIS   0.008   0.001   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6957)
  covalent geometry    : angle       0.97998 ( 9426)
  hydrogen bonds       : bond        0.03520 (  377)
  hydrogen bonds       : angle       3.64256 ( 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
  172 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 144
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ASN cc_start: 0.7916 (t0) cc_final: 0.7715 (t0)
REVERT: A  172 ASP cc_start: 0.8127 (m-30) cc_final: 0.7859 (m-30)
REVERT: A  218 PHE cc_start: 0.6625 (m-80) cc_final: 0.6299 (m-10)
REVERT: A  442 LEU cc_start: 0.8007 (mm) cc_final: 0.7578 (tp)
REVERT: A  587 TYR cc_start: 0.8044 (OUTLIER) cc_final: 0.6841 (m-80)
REVERT: A  732 MET cc_start: 0.8037 (mmm) cc_final: 0.7678 (mmt)
REVERT: A  901 SER cc_start: 0.9005 (m) cc_final: 0.8730 (t)
  outliers start: 28
  outliers final: 27
  residues processed: 161
  average time/residue: 0.0653
  time to fit residues: 14.8814
Evaluate side-chains
  168 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 140
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  110 ILE
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 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  256 THR
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 THR
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  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  580 ILE
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:    0.0040
   chunk 75 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 81 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 40 optimal weight:    0.4980
   chunk 68 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
A 418 ASN
** A 869 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 = 0.4043 r_free = 0.4043 target = 0.160271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.130131 restraints weight = 11488.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.133253 restraints weight = 6914.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.133972 restraints weight = 4698.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.134237 restraints weight = 4363.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.134358 restraints weight = 4136.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.5897

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= 0.139
  Angle     :  0.977  29.654   9426  Z= 0.416
  Chirality :  0.043   0.157   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.261  82.590    948
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 26.01 %
    Favored  : 69.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.30), residues: 886
  helix:  1.69 (0.25), residues: 461
  sheet: -1.31 (0.57), residues: 91
  loop : -0.76 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 153 
 TYR   0.013   0.001   TYR A 618 
 PHE   0.013   0.001   PHE A  63 
 TRP   0.031   0.002   TRP A 795 
 HIS   0.009   0.002   HIS A  98 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6957)
  covalent geometry    : angle       0.97697 ( 9426)
  hydrogen bonds       : bond        0.03607 (  377)
  hydrogen bonds       : angle       3.65642 ( 1137)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1185.93 seconds
wall clock time: 21 minutes 9.23 seconds (1269.23 seconds total)