Starting phenix.real_space_refine
on Fri Jul 25 03:40:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iww_35781/07_2025/8iww_35781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iww_35781/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iww_35781/07_2025/8iww_35781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iww_35781/07_2025/8iww_35781.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iww_35781/07_2025/8iww_35781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iww_35781/07_2025/8iww_35781.cif"
  }
  resolution = 3.71
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.015
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.20, per 1000 atoms: 0.76
  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: 1.76
  Conformation dependent library (CDL) restraints added in 961.0 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 8 sheets defined
      52.8% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  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: 2.47

  Time building geometry restraints manager: 2.13 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:             1.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.580
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.100
-------------------------------------------------------------------------------
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 : 9.22
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (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
 TRP   0.004   0.000   TRP A 460 
 HIS   0.001   0.000   HIS A 624 
 PHE   0.009   0.001   PHE A 176 
 TYR   0.005   0.001   TYR A 493 
 ARG   0.002   0.000   ARG A 842 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12863 (  377)
  hydrogen bonds       : angle       5.28723 ( 1137)
  covalent geometry    : bond        0.00336 ( 6957)
  covalent geometry    : angle       1.22125 ( 9426)

*********************** 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  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 MET cc_start: 0.3927 (mmm) cc_final: 0.3188 (mmp)
REVERT: A   81 ASN cc_start: 0.6219 (t0) cc_final: 0.5666 (m-40)
REVERT: A  110 ILE cc_start: 0.8752 (tt) cc_final: 0.8477 (tt)
REVERT: A  172 ASP cc_start: 0.7591 (m-30) cc_final: 0.7287 (m-30)
REVERT: A  355 LEU cc_start: 0.8674 (tp) cc_final: 0.7621 (tp)
REVERT: A  452 TYR cc_start: 0.6880 (m-80) cc_final: 0.6307 (m-80)
REVERT: A  510 TYR cc_start: 0.8759 (m-10) cc_final: 0.8448 (m-80)
REVERT: A  725 PHE cc_start: 0.3823 (m-80) cc_final: 0.3001 (m-80)
REVERT: A  834 PHE cc_start: 0.7042 (m-80) cc_final: 0.6567 (m-10)
REVERT: A  881 LEU cc_start: 0.8436 (mt) cc_final: 0.8027 (mp)
  outliers start: 1
  outliers final: 0
  residues processed: 249
  average time/residue: 0.2497
  time to fit residues: 78.4949
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  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0470
   chunk 23 optimal weight:    0.0980
   chunk 45 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 26 optimal weight:    0.1980
   chunk 42 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   overall best weight:    0.6480

-------------------------------------------------------------------------------
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 = 0.4220 r_free = 0.4220 target = 0.176502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.148689 restraints weight = 11502.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.148516 restraints weight = 8330.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.150959 restraints weight = 7020.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6957  Z= 0.152
  Angle     :  0.946  32.993   9426  Z= 0.402
  Chirality :  0.042   0.139   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.258  92.474    948
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 14.64 %
    Favored  : 82.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.28), residues: 886
  helix:  0.94 (0.24), residues: 452
  sheet: -1.31 (0.49), residues: 111
  loop : -1.42 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 795 
 HIS   0.003   0.001   HIS A  58 
 PHE   0.018   0.002   PHE A 538 
 TYR   0.023   0.002   TYR A 618 
 ARG   0.005   0.001   ARG A 143 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03583 (  377)
  hydrogen bonds       : angle       3.87641 ( 1137)
  covalent geometry    : bond        0.00349 ( 6957)
  covalent geometry    : angle       0.94580 ( 9426)

*********************** 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: 24
    poor density    : 165
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 MET cc_start: 0.3809 (mmm) cc_final: 0.3584 (mmm)
REVERT: A   81 ASN cc_start: 0.6055 (t0) cc_final: 0.5773 (m-40)
REVERT: A  110 ILE cc_start: 0.8623 (tt) cc_final: 0.8372 (tt)
REVERT: A  452 TYR cc_start: 0.7023 (m-80) cc_final: 0.6421 (m-80)
REVERT: A  510 TYR cc_start: 0.8964 (m-10) cc_final: 0.8590 (m-80)
REVERT: A  568 MET cc_start: 0.8172 (tpt) cc_final: 0.6803 (tpt)
REVERT: A  784 ILE cc_start: 0.9005 (tp) cc_final: 0.8791 (tp)
REVERT: A  834 PHE cc_start: 0.7169 (m-80) cc_final: 0.6907 (m-10)
REVERT: A  868 PHE cc_start: 0.6626 (OUTLIER) cc_final: 0.5126 (t80)
REVERT: A  881 LEU cc_start: 0.8257 (mt) cc_final: 0.8002 (mp)
REVERT: A  901 SER cc_start: 0.8881 (m) cc_final: 0.8531 (t)
  outliers start: 24
  outliers final: 17
  residues processed: 179
  average time/residue: 0.1967
  time to fit residues: 46.5156
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  : 0.595 
-------------------------------------------------------------------------------
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 22 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 83 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 82 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 855 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.165704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.132949 restraints weight = 11828.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.135068 restraints weight = 7579.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.135988 restraints weight = 5863.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6957  Z= 0.150
  Angle     :  0.943  29.610   9426  Z= 0.397
  Chirality :  0.042   0.158   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.288  93.395    948
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 17.52 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.29), residues: 886
  helix:  1.30 (0.24), residues: 454
  sheet: -1.45 (0.48), residues: 117
  loop : -1.17 (0.36), residues: 315

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03668 (  377)
  hydrogen bonds       : angle       3.79902 ( 1137)
  covalent geometry    : bond        0.00354 ( 6957)
  covalent geometry    : angle       0.94300 ( 9426)

*********************** 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
  190 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 159
  time to evaluate  : 0.796 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6231 (t0) cc_final: 0.5920 (m-40)
REVERT: A  784 ILE cc_start: 0.9043 (tp) cc_final: 0.8831 (tp)
REVERT: A  896 LYS cc_start: 0.6845 (tptp) cc_final: 0.6570 (mmmt)
REVERT: A  901 SER cc_start: 0.8875 (m) cc_final: 0.8566 (t)
  outliers start: 31
  outliers final: 22
  residues processed: 175
  average time/residue: 0.1921
  time to fit residues: 44.8027
Evaluate side-chains
  160 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.726 
-------------------------------------------------------------------------------
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  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  332 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  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  587 TYR
Chi-restraints excluded: chain A residue  675 MET
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 50 optimal weight:    0.7980
   chunk 58 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0270
   chunk 3 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.6238

-------------------------------------------------------------------------------
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 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 249 GLN
A 494 GLN
** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 855 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.162328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.131204 restraints weight = 11699.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.133762 restraints weight = 7434.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.135060 restraints weight = 5539.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.4398

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= 0.134
  Angle     :  0.923  29.603   9426  Z= 0.386
  Chirality :  0.041   0.151   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.293  92.889    948
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 21.44 %
    Favored  : 75.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.30), residues: 886
  helix:  1.60 (0.25), residues: 459
  sheet: -1.28 (0.52), residues: 108
  loop : -1.12 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 795 
 HIS   0.008   0.001   HIS A  98 
 PHE   0.018   0.001   PHE A 245 
 TYR   0.015   0.001   TYR A 618 
 ARG   0.008   0.001   ARG A 900 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03594 (  377)
  hydrogen bonds       : angle       3.68556 ( 1137)
  covalent geometry    : bond        0.00311 ( 6957)
  covalent geometry    : angle       0.92297 ( 9426)

*********************** 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  : 0.763 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6016 (t0) cc_final: 0.5761 (m-40)
REVERT: A  281 MET cc_start: 0.7061 (tpt) cc_final: 0.6825 (tpt)
REVERT: A  435 MET cc_start: 0.7442 (ptt) cc_final: 0.7089 (ptt)
REVERT: A  442 LEU cc_start: 0.7936 (mm) cc_final: 0.7457 (tp)
REVERT: A  784 ILE cc_start: 0.9079 (tp) cc_final: 0.8872 (tp)
  outliers start: 24
  outliers final: 18
  residues processed: 173
  average time/residue: 0.1886
  time to fit residues: 43.4247
Evaluate side-chains
  155 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 GLU
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  675 MET
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  855 GLN
Chi-restraints excluded: chain A residue  856 LEU
Chi-restraints excluded: chain A residue  876 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 6 optimal weight:    0.3980
   chunk 0 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
A 149 HIS
A 364 HIS
A 730 ASN
** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.158864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.128333 restraints weight = 11540.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.128656 restraints weight = 8657.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.130608 restraints weight = 7105.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.4822

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= 0.148
  Angle     :  0.933  29.661   9426  Z= 0.390
  Chirality :  0.041   0.153   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.360  92.827    948
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 22.35 %
    Favored  : 73.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.30), residues: 886
  helix:  1.57 (0.25), residues: 466
  sheet: -1.78 (0.52), residues: 107
  loop : -0.89 (0.38), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A  72 
 HIS   0.011   0.002   HIS A  98 
 PHE   0.009   0.001   PHE A 245 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.005   0.000   ARG A 900 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03711 (  377)
  hydrogen bonds       : angle       3.71475 ( 1137)
  covalent geometry    : bond        0.00346 ( 6957)
  covalent geometry    : angle       0.93328 ( 9426)

*********************** 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
  189 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 157
  time to evaluate  : 0.705 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6035 (t0) cc_final: 0.5750 (m-40)
REVERT: A  100 PHE cc_start: 0.7204 (m-10) cc_final: 0.6906 (m-80)
REVERT: A  435 MET cc_start: 0.7481 (ptt) cc_final: 0.7178 (ptt)
REVERT: A  442 LEU cc_start: 0.7950 (mm) cc_final: 0.7536 (tp)
  outliers start: 32
  outliers final: 21
  residues processed: 175
  average time/residue: 0.1800
  time to fit residues: 42.0708
Evaluate side-chains
  161 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  707 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0980
   chunk 39 optimal weight:    0.0470
   chunk 88 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.5478

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.159020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.126548 restraints weight = 11650.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.128726 restraints weight = 7566.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.129730 restraints weight = 5794.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.5044

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= 0.130
  Angle     :  0.933  29.530   9426  Z= 0.390
  Chirality :  0.042   0.158   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.302  91.025    948
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 25.36 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.30), residues: 886
  helix:  1.63 (0.25), residues: 466
  sheet: -1.57 (0.55), residues: 97
  loop : -0.89 (0.37), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A  72 
 HIS   0.012   0.002   HIS A  98 
 PHE   0.011   0.001   PHE A 245 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.004   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03527 (  377)
  hydrogen bonds       : angle       3.68728 ( 1137)
  covalent geometry    : bond        0.00300 ( 6957)
  covalent geometry    : angle       0.93252 ( 9426)

*********************** 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
  171 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6146 (t0) cc_final: 0.5799 (m-40)
REVERT: A  100 PHE cc_start: 0.7332 (m-10) cc_final: 0.6950 (m-80)
REVERT: A  218 PHE cc_start: 0.6765 (m-80) cc_final: 0.6265 (m-80)
REVERT: A  219 MET cc_start: 0.8254 (ppp) cc_final: 0.7906 (ppp)
REVERT: A  435 MET cc_start: 0.7598 (ptt) cc_final: 0.7374 (ptt)
REVERT: A  442 LEU cc_start: 0.7973 (mm) cc_final: 0.7659 (tp)
REVERT: A  568 MET cc_start: 0.8368 (tpt) cc_final: 0.7574 (tpt)
REVERT: A  671 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7412 (tm-30)
REVERT: A  732 MET cc_start: 0.8082 (mmm) cc_final: 0.7813 (mmt)
REVERT: A  829 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7756 (mm-40)
REVERT: A  902 ARG cc_start: 0.8319 (tpp80) cc_final: 0.7748 (mmm-85)
  outliers start: 23
  outliers final: 18
  residues processed: 162
  average time/residue: 0.1752
  time to fit residues: 38.7334
Evaluate side-chains
  155 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  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  583 ARG
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  856 LEU
Chi-restraints excluded: chain A residue  873 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 84 optimal weight:    0.0470
   chunk 54 optimal weight:    0.0970
   chunk 85 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   overall best weight:    0.5676

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.156543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.124256 restraints weight = 11596.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.127167 restraints weight = 7236.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.127527 restraints weight = 5068.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.5261

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= 0.131
  Angle     :  0.943  29.561   9426  Z= 0.392
  Chirality :  0.042   0.154   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.281  89.962    948
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 25.10 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.30), residues: 886
  helix:  1.66 (0.25), residues: 467
  sheet: -1.60 (0.55), residues: 97
  loop : -0.85 (0.38), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A  72 
 HIS   0.013   0.002   HIS A  98 
 PHE   0.009   0.001   PHE A 702 
 TYR   0.012   0.001   TYR A 618 
 ARG   0.003   0.000   ARG A 900 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03493 (  377)
  hydrogen bonds       : angle       3.68285 ( 1137)
  covalent geometry    : bond        0.00301 ( 6957)
  covalent geometry    : angle       0.94317 ( 9426)

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

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 147
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6095 (t0) cc_final: 0.5805 (m-40)
REVERT: A  125 GLU cc_start: 0.5550 (pt0) cc_final: 0.4965 (pt0)
REVERT: A  218 PHE cc_start: 0.6817 (m-80) cc_final: 0.6343 (m-80)
REVERT: A  219 MET cc_start: 0.8258 (ppp) cc_final: 0.7948 (ppp)
REVERT: A  264 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8439 (tt)
REVERT: A  435 MET cc_start: 0.7647 (ptt) cc_final: 0.7430 (ptt)
REVERT: A  442 LEU cc_start: 0.7905 (mm) cc_final: 0.7599 (tp)
REVERT: A  568 MET cc_start: 0.8398 (tpt) cc_final: 0.7729 (tpt)
REVERT: A  671 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7469 (tm-30)
REVERT: A  901 SER cc_start: 0.8948 (t) cc_final: 0.8604 (t)
  outliers start: 31
  outliers final: 23
  residues processed: 166
  average time/residue: 0.1717
  time to fit residues: 38.8002
Evaluate side-chains
  163 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  583 ARG
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  807 ASP
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  873 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0040
   chunk 28 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.6392

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.157188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.124720 restraints weight = 11591.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.127093 restraints weight = 7723.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.127974 restraints weight = 5496.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.5471

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= 0.137
  Angle     :  0.945  29.611   9426  Z= 0.398
  Chirality :  0.042   0.156   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.319  89.084    948
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 26.27 %
    Favored  : 70.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.30), residues: 886
  helix:  1.70 (0.25), residues: 467
  sheet: -1.52 (0.55), residues: 97
  loop : -0.83 (0.38), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP A  72 
 HIS   0.007   0.001   HIS A  98 
 PHE   0.009   0.001   PHE A 702 
 TYR   0.012   0.001   TYR A 618 
 ARG   0.002   0.000   ARG A 900 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03610 (  377)
  hydrogen bonds       : angle       3.66041 ( 1137)
  covalent geometry    : bond        0.00318 ( 6957)
  covalent geometry    : angle       0.94527 ( 9426)

*********************** 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
  177 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6093 (t0) cc_final: 0.5805 (m-40)
REVERT: A  218 PHE cc_start: 0.6684 (m-80) cc_final: 0.6297 (m-80)
REVERT: A  219 MET cc_start: 0.8200 (ppp) cc_final: 0.7949 (ppp)
REVERT: A  442 LEU cc_start: 0.8000 (mm) cc_final: 0.7633 (tp)
REVERT: A  842 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.7331 (mmm-85)
REVERT: A  901 SER cc_start: 0.9001 (t) cc_final: 0.8655 (t)
  outliers start: 28
  outliers final: 24
  residues processed: 164
  average time/residue: 0.1776
  time to fit residues: 39.2382
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  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  225 CYS
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  583 ARG
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  807 ASP
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 52 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 13 optimal weight:    0.1980
   chunk 59 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 73 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 53 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   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  61 ASN
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 730 ASN

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 = 0.158565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.126823 restraints weight = 11719.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.127632 restraints weight = 8054.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.128981 restraints weight = 6574.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.5578

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= 0.136
  Angle     :  0.965  29.631   9426  Z= 0.407
  Chirality :  0.042   0.146   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.312  87.495    948
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 25.88 %
    Favored  : 70.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.30), residues: 886
  helix:  1.67 (0.25), residues: 467
  sheet: -1.33 (0.58), residues: 91
  loop : -0.82 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A  72 
 HIS   0.007   0.001   HIS A  98 
 PHE   0.010   0.001   PHE A 702 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.004   0.000   ARG A 468 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03601 (  377)
  hydrogen bonds       : angle       3.66965 ( 1137)
  covalent geometry    : bond        0.00317 ( 6957)
  covalent geometry    : angle       0.96549 ( 9426)

*********************** 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
  181 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 150
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 LYS cc_start: 0.8241 (mtmm) cc_final: 0.8005 (mtmm)
REVERT: A   81 ASN cc_start: 0.6058 (t0) cc_final: 0.5753 (m-40)
REVERT: A  218 PHE cc_start: 0.6660 (m-80) cc_final: 0.6287 (m-80)
REVERT: A  219 MET cc_start: 0.8158 (ppp) cc_final: 0.7919 (ppp)
REVERT: A  435 MET cc_start: 0.7089 (ptt) cc_final: 0.6781 (ptt)
REVERT: A  442 LEU cc_start: 0.8173 (mm) cc_final: 0.7842 (tp)
REVERT: A  587 TYR cc_start: 0.8103 (OUTLIER) cc_final: 0.6825 (m-80)
REVERT: A  757 ASP cc_start: 0.6720 (m-30) cc_final: 0.6442 (m-30)
REVERT: A  842 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7304 (mmm-85)
REVERT: A  901 SER cc_start: 0.8999 (t) cc_final: 0.8671 (t)
  outliers start: 31
  outliers final: 26
  residues processed: 166
  average time/residue: 0.1738
  time to fit residues: 39.3409
Evaluate side-chains
  171 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  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  580 ILE
Chi-restraints excluded: chain A residue  583 ARG
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  807 ASP
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 26 optimal weight:    0.9980
   chunk 63 optimal weight:    0.6980
   chunk 2 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    8.9990
   chunk 33 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 418 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.157524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.125566 restraints weight = 11854.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.126784 restraints weight = 8788.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.127700 restraints weight = 6637.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.5837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6957  Z= 0.152
  Angle     :  0.980  29.609   9426  Z= 0.419
  Chirality :  0.043   0.158   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.372  86.271    948
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 26.67 %
    Favored  : 69.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.30), residues: 886
  helix:  1.61 (0.25), residues: 461
  sheet: -1.40 (0.57), residues: 91
  loop : -0.76 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A  72 
 HIS   0.008   0.001   HIS A  98 
 PHE   0.011   0.001   PHE A 274 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.005   0.001   ARG A 902 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03965 (  377)
  hydrogen bonds       : angle       3.78159 ( 1137)
  covalent geometry    : bond        0.00357 ( 6957)
  covalent geometry    : angle       0.98013 ( 9426)

********************** 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
  180 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 149
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6039 (t0) cc_final: 0.5734 (m-40)
REVERT: A  175 LEU cc_start: 0.7965 (mm) cc_final: 0.7611 (mp)
REVERT: A  218 PHE cc_start: 0.6641 (m-80) cc_final: 0.6258 (m-80)
REVERT: A  435 MET cc_start: 0.7100 (ptt) cc_final: 0.6783 (ptt)
REVERT: A  442 LEU cc_start: 0.8106 (mm) cc_final: 0.7784 (tp)
REVERT: A  732 MET cc_start: 0.8055 (mmm) cc_final: 0.7823 (mmt)
REVERT: A  842 ARG cc_start: 0.7581 (mmm-85) cc_final: 0.7320 (mmm-85)
REVERT: A  901 SER cc_start: 0.9038 (t) cc_final: 0.8750 (t)
  outliers start: 31
  outliers final: 28
  residues processed: 166
  average time/residue: 0.1776
  time to fit residues: 40.3890
Evaluate side-chains
  174 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  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  583 ARG
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  807 ASP
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 30 optimal weight:    0.5980
   chunk 65 optimal weight:    0.2980
   chunk 42 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 39 optimal weight:    7.9990
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 ASN
A 855 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.159680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.129839 restraints weight = 11608.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.131314 restraints weight = 8321.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.132331 restraints weight = 6076.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.5878

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= 0.147
  Angle     :  0.996  29.586   9426  Z= 0.425
  Chirality :  0.044   0.169   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.366  85.050    948
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 27.45 %
    Favored  : 68.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.30), residues: 886
  helix:  1.63 (0.25), residues: 462
  sheet: -1.35 (0.56), residues: 92
  loop : -0.75 (0.37), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 795 
 HIS   0.009   0.001   HIS A  98 
 PHE   0.010   0.001   PHE A 702 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.008   0.001   ARG A 902 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03874 (  377)
  hydrogen bonds       : angle       3.81032 ( 1137)
  covalent geometry    : bond        0.00342 ( 6957)
  covalent geometry    : angle       0.99558 ( 9426)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2724.82 seconds
wall clock time: 48 minutes 19.73 seconds (2899.73 seconds total)