Starting phenix.real_space_refine
on Sat May 10 22:47:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iww_35781/05_2025/8iww_35781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iww_35781/05_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_35781/05_2025/8iww_35781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iww_35781/05_2025/8iww_35781.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iww_35781/05_2025/8iww_35781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iww_35781/05_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-5687/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: 4.62, per 1000 atoms: 0.67
  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: 1.54
  Conformation dependent library (CDL) restraints added in 910.7 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: 0.78
  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: 2.26

  Time building geometry restraints manager: 1.83 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:             2.480
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     19.050
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.780
-------------------------------------------------------------------------------
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  : 0.610 
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: 0.2341
  time to fit residues: 73.7912
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  : 0.772 
-------------------------------------------------------------------------------
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 = 0.148528 restraints weight = 8330.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.150961 restraints weight = 7019.288|
|-----------------------------------------------------------------------------|
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  : 0.794 
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: 0.3583 (mmm)
REVERT: A   81 ASN cc_start: 0.6055 (t0) cc_final: 0.5774 (m-40)
REVERT: A  110 ILE cc_start: 0.8622 (tt) cc_final: 0.8371 (tt)
REVERT: A  452 TYR cc_start: 0.7023 (m-80) cc_final: 0.6422 (m-80)
REVERT: A  510 TYR cc_start: 0.8963 (m-10) cc_final: 0.8589 (m-80)
REVERT: A  568 MET cc_start: 0.8170 (tpt) cc_final: 0.6803 (tpt)
REVERT: A  784 ILE cc_start: 0.9005 (tp) cc_final: 0.8792 (tp)
REVERT: A  834 PHE cc_start: 0.7169 (m-80) cc_final: 0.6906 (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: 0.1933
  time to fit residues: 45.6045
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  : 0.729 
-------------------------------------------------------------------------------
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:    0.0020
   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:    0.2980
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.5588

-------------------------------------------------------------------------------
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 = 0.4100 r_free = 0.4100 target = 0.165917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.135303 restraints weight = 11744.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.137528 restraints weight = 7321.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.138404 restraints weight = 5270.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.3771

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= 0.131
  Angle     :  0.933  29.458   9426  Z= 0.389
  Chirality :  0.042   0.145   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.222  92.117    948
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 18.30 %
    Favored  : 78.56 %
  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:  0.09 (0.29), residues: 886
  helix:  1.39 (0.24), residues: 448
  sheet: -1.51 (0.48), residues: 119
  loop : -1.19 (0.36), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 795 
 HIS   0.007   0.001   HIS A  98 
 PHE   0.013   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        0.03439 (  377)
  hydrogen bonds       : angle       3.75119 ( 1137)
  covalent geometry    : bond        0.00305 ( 6957)
  covalent geometry    : angle       0.93295 ( 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
  182 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 158
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 MET cc_start: 0.3621 (mmm) cc_final: 0.3416 (mmm)
REVERT: A   81 ASN cc_start: 0.6194 (t0) cc_final: 0.5865 (m-40)
REVERT: A  784 ILE cc_start: 0.9037 (tp) cc_final: 0.8829 (tp)
REVERT: A  834 PHE cc_start: 0.7271 (m-80) cc_final: 0.7070 (m-10)
REVERT: A  901 SER cc_start: 0.8856 (m) cc_final: 0.8558 (t)
  outliers start: 24
  outliers final: 16
  residues processed: 169
  average time/residue: 0.1775
  time to fit residues: 40.1907
Evaluate side-chains
  155 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  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  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  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:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 11 optimal weight:    6.9990
   chunk 85 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   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  61 ASN
** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 249 GLN
A 494 GLN
A 730 ASN
** A 841 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 855 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.162374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.130612 restraints weight = 11742.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.131559 restraints weight = 8789.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.132892 restraints weight = 6509.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.4546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6957  Z= 0.148
  Angle     :  0.937  29.733   9426  Z= 0.396
  Chirality :  0.042   0.151   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.326  93.065    948
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 20.78 %
    Favored  : 75.16 %
  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:  0.35 (0.30), residues: 886
  helix:  1.57 (0.25), residues: 461
  sheet: -1.79 (0.50), residues: 107
  loop : -0.98 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 795 
 HIS   0.007   0.001   HIS A  98 
 PHE   0.018   0.002   PHE A 245 
 TYR   0.014   0.001   TYR A 618 
 ARG   0.003   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03672 (  377)
  hydrogen bonds       : angle       3.67058 ( 1137)
  covalent geometry    : bond        0.00345 ( 6957)
  covalent geometry    : angle       0.93717 ( 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
  190 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 159
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 MET cc_start: 0.4022 (mmm) cc_final: 0.3798 (mmm)
REVERT: A   81 ASN cc_start: 0.6100 (t0) cc_final: 0.5808 (m-40)
REVERT: A  435 MET cc_start: 0.7450 (ptt) cc_final: 0.7121 (ptt)
REVERT: A  442 LEU cc_start: 0.8005 (mm) cc_final: 0.7493 (tp)
REVERT: A  732 MET cc_start: 0.7921 (mmm) cc_final: 0.7712 (mmt)
REVERT: A  881 LEU cc_start: 0.8384 (mp) cc_final: 0.8061 (mp)
REVERT: A  901 SER cc_start: 0.8901 (m) cc_final: 0.8583 (t)
  outliers start: 31
  outliers final: 21
  residues processed: 179
  average time/residue: 0.1831
  time to fit residues: 43.8450
Evaluate side-chains
  158 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 137
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   74 LYS
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  191 GLU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  337 ILE
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  396 PHE
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  855 GLN
Chi-restraints excluded: chain A residue  856 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 75 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.1182

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.155141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.123220 restraints weight = 11578.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.125245 restraints weight = 7603.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.126019 restraints weight = 6032.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.5190

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= 0.182
  Angle     :  0.966  29.902   9426  Z= 0.414
  Chirality :  0.043   0.175   1131
  Planarity :  0.004   0.046   1186
  Dihedral  :  5.556  94.119    948
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 22.75 %
    Favored  : 72.81 %
  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:  0.27 (0.30), residues: 886
  helix:  1.45 (0.25), residues: 467
  sheet: -1.82 (0.51), residues: 107
  loop : -0.97 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A  72 
 HIS   0.010   0.002   HIS A  98 
 PHE   0.011   0.002   PHE A 818 
 TYR   0.013   0.002   TYR A 618 
 ARG   0.004   0.001   ARG A 827 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04195 (  377)
  hydrogen bonds       : angle       3.82294 ( 1137)
  covalent geometry    : bond        0.00428 ( 6957)
  covalent geometry    : angle       0.96645 ( 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
  193 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 159
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6133 (t0) cc_final: 0.5808 (m-40)
REVERT: A  100 PHE cc_start: 0.7247 (m-10) cc_final: 0.6910 (m-80)
REVERT: A  175 LEU cc_start: 0.7765 (mm) cc_final: 0.7443 (mp)
REVERT: A  218 PHE cc_start: 0.6763 (m-80) cc_final: 0.6341 (m-80)
REVERT: A  435 MET cc_start: 0.7457 (ptt) cc_final: 0.7203 (ptt)
REVERT: A  442 LEU cc_start: 0.8137 (mm) cc_final: 0.7683 (tp)
REVERT: A  881 LEU cc_start: 0.8370 (mp) cc_final: 0.8132 (mp)
REVERT: A  901 SER cc_start: 0.8974 (m) cc_final: 0.8656 (t)
  outliers start: 34
  outliers final: 26
  residues processed: 179
  average time/residue: 0.1790
  time to fit residues: 42.7326
Evaluate side-chains
  161 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 135
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  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  338 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  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  807 ASP
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:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0060
   chunk 88 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 51 optimal weight:    0.4980
   chunk 25 optimal weight:    0.6980
   overall best weight:    0.6196

-------------------------------------------------------------------------------
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 855 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 = 0.3985 r_free = 0.3985 target = 0.156562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.122586 restraints weight = 11620.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.125960 restraints weight = 7048.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.128248 restraints weight = 5073.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.5392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6957  Z= 0.135
  Angle     :  0.943  29.592   9426  Z= 0.397
  Chirality :  0.042   0.160   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.438  92.358    948
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 24.58 %
    Favored  : 72.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.45 (0.30), residues: 886
  helix:  1.60 (0.25), residues: 466
  sheet: -1.68 (0.54), residues: 97
  loop : -0.94 (0.37), residues: 323

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   0.011   0.001   PHE A 454 
 TYR   0.014   0.001   TYR A 618 
 ARG   0.008   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03741 (  377)
  hydrogen bonds       : angle       3.72238 ( 1137)
  covalent geometry    : bond        0.00312 ( 6957)
  covalent geometry    : angle       0.94285 ( 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
  173 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.689 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6094 (t0) cc_final: 0.5783 (m-40)
REVERT: A  175 LEU cc_start: 0.7927 (mm) cc_final: 0.7580 (mp)
REVERT: A  218 PHE cc_start: 0.6886 (m-80) cc_final: 0.6414 (m-80)
REVERT: A  281 MET cc_start: 0.7395 (tpt) cc_final: 0.7192 (tpt)
REVERT: A  442 LEU cc_start: 0.8028 (mm) cc_final: 0.7740 (tp)
REVERT: A  568 MET cc_start: 0.8426 (tpt) cc_final: 0.7721 (tpt)
REVERT: A  901 SER cc_start: 0.9028 (m) cc_final: 0.8710 (t)
  outliers start: 26
  outliers final: 18
  residues processed: 165
  average time/residue: 0.1662
  time to fit residues: 37.2958
Evaluate side-chains
  156 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  583 ARG
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  788 CYS
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  856 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 81 optimal weight:    0.1980
   chunk 23 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0020
   chunk 28 optimal weight:    0.0970
   chunk 84 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 85 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.3786

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

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 = 0.158094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.127247 restraints weight = 11530.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.128441 restraints weight = 7400.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.129866 restraints weight = 6222.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.5448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6957  Z= 0.121
  Angle     :  0.944  29.631   9426  Z= 0.393
  Chirality :  0.042   0.152   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.340  89.977    948
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 25.10 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.64 (0.30), residues: 886
  helix:  1.78 (0.25), residues: 460
  sheet: -1.63 (0.54), residues: 97
  loop : -0.84 (0.37), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A  72 
 HIS   0.010   0.001   HIS A  98 
 PHE   0.010   0.001   PHE A 454 
 TYR   0.014   0.001   TYR A 618 
 ARG   0.006   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03506 (  377)
  hydrogen bonds       : angle       3.66216 ( 1137)
  covalent geometry    : bond        0.00272 ( 6957)
  covalent geometry    : angle       0.94418 ( 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
  177 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 149
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6062 (t0) cc_final: 0.5747 (m-40)
REVERT: A  218 PHE cc_start: 0.6746 (m-80) cc_final: 0.6326 (m-80)
REVERT: A  442 LEU cc_start: 0.7978 (mm) cc_final: 0.7678 (tp)
REVERT: A  568 MET cc_start: 0.8280 (tpt) cc_final: 0.7661 (tpt)
REVERT: A  587 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.6799 (m-80)
REVERT: A  901 SER cc_start: 0.9062 (m) cc_final: 0.8737 (t)
  outliers start: 28
  outliers final: 20
  residues processed: 167
  average time/residue: 0.1831
  time to fit residues: 41.5176
Evaluate side-chains
  163 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  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  467 HIS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  583 ARG
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  807 ASP
Chi-restraints excluded: chain A residue  856 LEU
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 79 optimal weight:    0.4980
   chunk 76 optimal weight:    0.6980
   chunk 62 optimal weight:    0.2980
   chunk 3 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0770
   chunk 28 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.4738

-------------------------------------------------------------------------------
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 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.159690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.129189 restraints weight = 11582.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.130833 restraints weight = 7817.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.132101 restraints weight = 6321.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.5588

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= 0.126
  Angle     :  0.950  29.639   9426  Z= 0.399
  Chirality :  0.042   0.151   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.313  88.651    948
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 26.93 %
    Favored  : 69.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.66 (0.30), residues: 886
  helix:  1.78 (0.25), residues: 460
  sheet: -1.54 (0.55), residues: 97
  loop : -0.82 (0.37), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A  72 
 HIS   0.009   0.001   HIS A  98 
 PHE   0.009   0.001   PHE A 702 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.005   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03489 (  377)
  hydrogen bonds       : angle       3.64852 ( 1137)
  covalent geometry    : bond        0.00287 ( 6957)
  covalent geometry    : angle       0.94987 ( 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
  176 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 0.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6005 (t0) cc_final: 0.5709 (m-40)
REVERT: A  218 PHE cc_start: 0.6661 (m-80) cc_final: 0.6306 (m-80)
REVERT: A  442 LEU cc_start: 0.7969 (mm) cc_final: 0.7692 (tp)
REVERT: A  587 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.6837 (m-80)
REVERT: A  901 SER cc_start: 0.9062 (m) cc_final: 0.8763 (t)
  outliers start: 28
  outliers final: 24
  residues processed: 166
  average time/residue: 0.1702
  time to fit residues: 38.6161
Evaluate side-chains
  165 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  388 VAL
Chi-restraints excluded: chain A residue  415 VAL
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  467 HIS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  583 ARG
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  675 MET
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  807 ASP
Chi-restraints excluded: chain A residue  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:    0.9980
   chunk 30 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 13 optimal weight:    0.3980
   chunk 59 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 29 optimal weight:    0.3980
   chunk 53 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.158399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.126263 restraints weight = 11787.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.128637 restraints weight = 7747.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.130133 restraints weight = 5695.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.5772

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= 0.136
  Angle     :  0.959  29.633   9426  Z= 0.404
  Chirality :  0.043   0.161   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.358  87.548    948
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 26.80 %
    Favored  : 69.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.68 (0.30), residues: 886
  helix:  1.72 (0.25), residues: 461
  sheet: -1.43 (0.57), residues: 91
  loop : -0.76 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A  72 
 HIS   0.011   0.001   HIS A  98 
 PHE   0.009   0.001   PHE A 702 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.004   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03666 (  377)
  hydrogen bonds       : angle       3.68658 ( 1137)
  covalent geometry    : bond        0.00314 ( 6957)
  covalent geometry    : angle       0.95893 ( 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
  178 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 146
  time to evaluate  : 0.703 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6082 (t0) cc_final: 0.5737 (m-40)
REVERT: A  175 LEU cc_start: 0.8033 (mm) cc_final: 0.7627 (mp)
REVERT: A  218 PHE cc_start: 0.6831 (m-80) cc_final: 0.6415 (m-80)
REVERT: A  281 MET cc_start: 0.7425 (tpt) cc_final: 0.7167 (tpt)
REVERT: A  442 LEU cc_start: 0.7868 (mm) cc_final: 0.7651 (tp)
REVERT: A  587 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.6856 (m-80)
REVERT: A  901 SER cc_start: 0.9043 (m) cc_final: 0.8720 (t)
  outliers start: 32
  outliers final: 26
  residues processed: 164
  average time/residue: 0.1772
  time to fit residues: 39.4464
Evaluate side-chains
  168 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 141
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  286 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  467 HIS
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  490 CYS
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  583 ARG
Chi-restraints excluded: chain A residue  587 TYR
Chi-restraints excluded: chain A residue  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0980
   chunk 33 optimal weight:    0.2980
   chunk 50 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   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  58 HIS
A  61 ASN
** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 ASN
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.158416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.126444 restraints weight = 11736.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.128557 restraints weight = 7246.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.129533 restraints weight = 5515.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.5814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6957  Z= 0.137
  Angle     :  0.979  29.626   9426  Z= 0.415
  Chirality :  0.043   0.163   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.344  86.456    948
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 27.32 %
    Favored  : 68.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.64 (0.30), residues: 886
  helix:  1.75 (0.25), residues: 461
  sheet: -1.56 (0.55), residues: 97
  loop : -0.83 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 795 
 HIS   0.010   0.001   HIS A  98 
 PHE   0.009   0.001   PHE A 702 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.009   0.001   ARG A 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  377)
  hydrogen bonds       : angle       3.69351 ( 1137)
  covalent geometry    : bond        0.00317 ( 6957)
  covalent geometry    : angle       0.97892 ( 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
  170 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.6141 (t0) cc_final: 0.5787 (m-40)
REVERT: A  175 LEU cc_start: 0.8057 (mm) cc_final: 0.7632 (mp)
REVERT: A  218 PHE cc_start: 0.6752 (m-80) cc_final: 0.6376 (m-80)
REVERT: A  274 PHE cc_start: 0.8496 (m-10) cc_final: 0.8226 (m-80)
REVERT: A  293 GLU cc_start: 0.7594 (pp20) cc_final: 0.7375 (pp20)
REVERT: A  467 HIS cc_start: 0.4944 (t70) cc_final: 0.4553 (t70)
REVERT: A  474 PRO cc_start: 0.8603 (Cg_exo) cc_final: 0.8396 (Cg_endo)
REVERT: A  587 TYR cc_start: 0.8127 (OUTLIER) cc_final: 0.6840 (m-80)
REVERT: A  901 SER cc_start: 0.9017 (m) cc_final: 0.8716 (t)
  outliers start: 29
  outliers final: 26
  residues processed: 159
  average time/residue: 0.1852
  time to fit residues: 40.0681
Evaluate side-chains
  165 residues out of total 765 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  130 GLU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  286 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  583 ARG
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  741 MET
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  852 ILE
Chi-restraints excluded: chain A residue  856 LEU
Chi-restraints excluded: chain A residue  857 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 30 optimal weight:    0.3980
   chunk 65 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    0.4980
   chunk 74 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 60 optimal weight:    0.1980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.161026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.131291 restraints weight = 11541.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.132627 restraints weight = 8466.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.134200 restraints weight = 6833.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.5853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6957  Z= 0.133
  Angle     :  0.973  29.624   9426  Z= 0.413
  Chirality :  0.043   0.190   1131
  Planarity :  0.004   0.045   1186
  Dihedral  :  5.312  84.953    948
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 27.58 %
    Favored  : 68.63 %
  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:  0.72 (0.30), residues: 886
  helix:  1.74 (0.25), residues: 467
  sheet: -1.33 (0.58), residues: 90
  loop : -0.80 (0.37), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 795 
 HIS   0.010   0.001   HIS A  98 
 PHE   0.009   0.001   PHE A 702 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.007   0.001   ARG A 902 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03555 (  377)
  hydrogen bonds       : angle       3.70664 ( 1137)
  covalent geometry    : bond        0.00304 ( 6957)
  covalent geometry    : angle       0.97292 ( 9426)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2496.17 seconds
wall clock time: 44 minutes 39.85 seconds (2679.85 seconds total)