Starting phenix.real_space_refine
on Wed May 21 15:15:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jgl_36238/05_2025/8jgl_36238_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jgl_36238/05_2025/8jgl_36238.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jgl_36238/05_2025/8jgl_36238.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jgl_36238/05_2025/8jgl_36238.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jgl_36238/05_2025/8jgl_36238_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jgl_36238/05_2025/8jgl_36238_trim.cif"
  }
  resolution = 3.14
  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=   0.038
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: 6
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      72      5.16       5
     C    7060      2.51       5
     N    1780      2.21       5
     O    1880      1.98       5
     H   10868      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 21662
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 10807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 684, 10807
          Classifications: {'peptide': 684}
          Link IDs: {'PTRANS': 28, 'TRANS': 655}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 10807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 684, 10807
          Classifications: {'peptide': 684}
          Link IDs: {'PTRANS': 28, 'TRANS': 655}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Classifications: {'RNA': 1}
          Modifications used: {'rna3p': 1}
    Chain: "B"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Classifications: {'RNA': 1}
          Modifications used: {'rna2p': 1}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 10.51, per 1000 atoms: 0.49
  Number of scatterers: 21662
  At special positions: 0
  Unit cell: (86.49, 121.83, 108.81, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      72     16.00
     P       2     15.00
     O    1880      8.00
     N    1780      7.00
     C    7060      6.00
     H   10868      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 161 " - pdb=" SG  CYS A 172 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 463 " - pdb=" SG  CYS A 472 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 562 " - pdb=" SG  CYS A 568 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 161 " - pdb=" SG  CYS B 172 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 463 " - pdb=" SG  CYS B 472 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 562 " - pdb=" SG  CYS B 568 " distance=2.03

  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: 5.64
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2520

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 6 sheets defined
      68.9% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 92 through 112
      removed outlier: 3.654A  pdb=" N   GLU A  96 " --> pdb=" O   ASP A  92 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LYS A 110 " --> pdb=" O   ARG A 106 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LYS A 112 " --> pdb=" O   ASN A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 157
      removed outlier: 4.501A  pdb=" N   GLY A 128 " --> pdb=" O   ASP A 124 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   TRP A 129 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LYS A 157 " --> pdb=" O   MET A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 175
    Processing helix  chain 'A' and resid 192 through 198
    Processing helix  chain 'A' and resid 203 through 233
    Processing helix  chain 'A' and resid 234 through 237
      removed outlier: 4.112A  pdb=" N   CYS A 237 " --> pdb=" O   PRO A 234 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 234 through 237'
    Processing helix  chain 'A' and resid 240 through 249
      removed outlier: 3.656A  pdb=" N   THR A 246 " --> pdb=" O   PRO A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 257
      removed outlier: 4.287A  pdb=" N   LEU A 257 " --> pdb=" O   ARG A 254 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 254 through 257'
    Processing helix  chain 'A' and resid 258 through 276
      removed outlier: 3.658A  pdb=" N   LEU A 262 " --> pdb=" O   GLY A 258 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLY A 276 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 298
      removed outlier: 4.145A  pdb=" N   HIS A 287 " --> pdb=" O   GLY A 283 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   TYR A 298 " --> pdb=" O   ASN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 305
      removed outlier: 3.504A  pdb=" N   THR A 305 " --> pdb=" O   PRO A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 327
    Processing helix  chain 'A' and resid 328 through 339
    Processing helix  chain 'A' and resid 347 through 365
      removed outlier: 4.150A  pdb=" N   ARG A 351 " --> pdb=" O   LYS A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 389 through 420
    Processing helix  chain 'A' and resid 421 through 425
    Processing helix  chain 'A' and resid 426 through 443
    Processing helix  chain 'A' and resid 445 through 450
      removed outlier: 3.549A  pdb=" N   LEU A 450 " --> pdb=" O   PRO A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 461
    Processing helix  chain 'A' and resid 469 through 473
      removed outlier: 3.910A  pdb=" N   ASP A 473 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 518
      removed outlier: 3.864A  pdb=" N   TYR A 497 " --> pdb=" O   GLY A 493 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   VAL A 515 " --> pdb=" O   ILE A 511 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   PHE A 516 " --> pdb=" O   ILE A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 552
    Processing helix  chain 'A' and resid 555 through 560
      removed outlier: 3.555A  pdb=" N   GLU A 560 " --> pdb=" O   PHE A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 588
      removed outlier: 3.679A  pdb=" N   TYR A 574 " --> pdb=" O   THR A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 601
    Processing helix  chain 'A' and resid 606 through 623
    Processing helix  chain 'A' and resid 628 through 638
    Processing helix  chain 'A' and resid 653 through 658
      removed outlier: 4.028A  pdb=" N   VAL A 657 " --> pdb=" O   LEU A 653 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 676 through 687
    Processing helix  chain 'A' and resid 709 through 722
    Processing helix  chain 'A' and resid 767 through 779
    Processing helix  chain 'A' and resid 797 through 805
    Processing helix  chain 'B' and resid 92 through 112
      removed outlier: 3.535A  pdb=" N   GLU B  96 " --> pdb=" O   ASP B  92 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LYS B 110 " --> pdb=" O   ARG B 106 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   LYS B 112 " --> pdb=" O   ASN B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 157
      removed outlier: 4.408A  pdb=" N   GLY B 128 " --> pdb=" O   ASP B 124 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   TRP B 129 " --> pdb=" O   ALA B 125 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS B 157 " --> pdb=" O   MET B 153 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 175
    Processing helix  chain 'B' and resid 192 through 198
    Processing helix  chain 'B' and resid 203 through 233
    Processing helix  chain 'B' and resid 234 through 237
      removed outlier: 4.111A  pdb=" N   CYS B 237 " --> pdb=" O   PRO B 234 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 234 through 237'
    Processing helix  chain 'B' and resid 240 through 249
      removed outlier: 3.602A  pdb=" N   THR B 246 " --> pdb=" O   PRO B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 257
      removed outlier: 3.507A  pdb=" N   TYR B 256 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   LEU B 257 " --> pdb=" O   ARG B 254 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 253 through 257'
    Processing helix  chain 'B' and resid 258 through 276
      removed outlier: 3.638A  pdb=" N   LEU B 262 " --> pdb=" O   GLY B 258 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   GLY B 276 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 298
      removed outlier: 4.130A  pdb=" N   HIS B 287 " --> pdb=" O   GLY B 283 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   TYR B 298 " --> pdb=" O   ASN B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 305
      removed outlier: 3.651A  pdb=" N   THR B 305 " --> pdb=" O   PRO B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 327
    Processing helix  chain 'B' and resid 328 through 339
    Processing helix  chain 'B' and resid 347 through 365
      removed outlier: 4.165A  pdb=" N   ARG B 351 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 388
      No H-bonds generated for 'chain 'B' and resid 386 through 388'
    Processing helix  chain 'B' and resid 389 through 418
    Processing helix  chain 'B' and resid 421 through 425
    Processing helix  chain 'B' and resid 426 through 443
    Processing helix  chain 'B' and resid 445 through 450
      removed outlier: 3.593A  pdb=" N   LEU B 450 " --> pdb=" O   PRO B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 461
    Processing helix  chain 'B' and resid 469 through 473
      removed outlier: 3.880A  pdb=" N   ASP B 473 " --> pdb=" O   SER B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 518
      removed outlier: 3.864A  pdb=" N   TYR B 497 " --> pdb=" O   GLY B 493 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL B 515 " --> pdb=" O   ILE B 511 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   PHE B 516 " --> pdb=" O   ILE B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 552
    Processing helix  chain 'B' and resid 555 through 560
      removed outlier: 3.544A  pdb=" N   GLU B 560 " --> pdb=" O   PHE B 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 570 through 588
      removed outlier: 3.669A  pdb=" N   TYR B 574 " --> pdb=" O   THR B 570 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 601
    Processing helix  chain 'B' and resid 606 through 623
    Processing helix  chain 'B' and resid 628 through 638
    Processing helix  chain 'B' and resid 676 through 687
    Processing helix  chain 'B' and resid 709 through 722
    Processing helix  chain 'B' and resid 767 through 779
      removed outlier: 3.501A  pdb=" N   VAL B 771 " --> pdb=" O   PRO B 767 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 797 through 805
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161
    Processing sheet with id=AA2, first strand: chain 'A' and resid 691 through 695
      removed outlier: 6.840A  pdb=" N   PHE A 692 " --> pdb=" O   PHE A 706 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   PHE A 706 " --> pdb=" O   PHE A 692 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL A 694 " --> pdb=" O   VAL A 704 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 761 through 763
      removed outlier: 5.937A  pdb=" N   VAL A 762 " --> pdb=" O   THR A 786 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   CYS A 783 " --> pdb=" O   ILE A 794 " (cutoff:3.500A)
      removed outlier: 4.847A  pdb=" N   ILE A 794 " --> pdb=" O   CYS A 783 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   VAL A 785 " --> pdb=" O   LEU A 792 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 160 through 161
    Processing sheet with id=AA5, first strand: chain 'B' and resid 691 through 695
      removed outlier: 6.786A  pdb=" N   PHE B 692 " --> pdb=" O   PHE B 706 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   PHE B 706 " --> pdb=" O   PHE B 692 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   VAL B 694 " --> pdb=" O   VAL B 704 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 782 through 787
      removed outlier: 6.648A  pdb=" N   CYS B 783 " --> pdb=" O   ILE B 794 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   ILE B 794 " --> pdb=" O   CYS B 783 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   VAL B 785 " --> pdb=" O   LEU B 792 " (cutoff:3.500A)

    658 hydrogen bonds defined for protein.
    1944 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: 7.56

  Time building geometry restraints manager: 6.76 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 10844
        1.03 -     1.23: 45
        1.23 -     1.43: 4655
        1.43 -     1.62: 6288
        1.62 -     1.82: 110
  Bond restraints: 21942
  Sorted by residual:
  bond pdb=" C4  AMP B 901 "
       pdb=" C5  AMP B 901 "
    ideal  model  delta    sigma   weight residual
    1.490  1.380  0.110 2.00e-02 2.50e+03 3.03e+01
  bond pdb=" C4  AMP A 901 "
       pdb=" C5  AMP A 901 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.97e+01
  bond pdb=" C5  AMP B 901 "
       pdb=" C6  AMP B 901 "
    ideal  model  delta    sigma   weight residual
    1.490  1.405  0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" C5  AMP A 901 "
       pdb=" C6  AMP A 901 "
    ideal  model  delta    sigma   weight residual
    1.490  1.408  0.082 2.00e-02 2.50e+03 1.67e+01
  bond pdb=" NZ  LYS A 245 "
       pdb=" HZ2 LYS A 245 "
    ideal  model  delta    sigma   weight residual
    0.890  0.961 -0.071 2.00e-02 2.50e+03 1.28e+01
  ... (remaining 21937 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 39433
        2.12 -     4.25: 198
        4.25 -     6.37: 21
        6.37 -     8.49: 12
        8.49 -    10.62: 6
  Bond angle restraints: 39670
  Sorted by residual:
  angle pdb=" CA  PRO B 767 "
        pdb=" N   PRO B 767 "
        pdb=" CD  PRO B 767 "
      ideal   model   delta    sigma   weight residual
     112.00  101.38   10.62 1.40e+00 5.10e-01 5.75e+01
  angle pdb=" CA  PRO A 767 "
        pdb=" N   PRO A 767 "
        pdb=" CD  PRO A 767 "
      ideal   model   delta    sigma   weight residual
     112.00  101.80   10.20 1.40e+00 5.10e-01 5.31e+01
  angle pdb=" N   GLU B 631 "
        pdb=" CA  GLU B 631 "
        pdb=" C   GLU B 631 "
      ideal   model   delta    sigma   weight residual
     113.55  106.64    6.91 1.26e+00 6.30e-01 3.01e+01
  angle pdb=" N   GLU A 631 "
        pdb=" CA  GLU A 631 "
        pdb=" C   GLU A 631 "
      ideal   model   delta    sigma   weight residual
     113.12  106.59    6.53 1.25e+00 6.40e-01 2.73e+01
  angle pdb=" N   GLU B 339 "
        pdb=" CA  GLU B 339 "
        pdb=" C   GLU B 339 "
      ideal   model   delta    sigma   weight residual
     111.40  117.30   -5.90 1.22e+00 6.72e-01 2.34e+01
  ... (remaining 39665 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 9253
       17.98 -    35.96: 713
       35.96 -    53.94: 255
       53.94 -    71.91: 66
       71.91 -    89.89: 17
  Dihedral angle restraints: 10304
    sinusoidal: 5472
      harmonic: 4832
  Sorted by residual:
  dihedral pdb=" CA  ARG B 659 "
           pdb=" C   ARG B 659 "
           pdb=" N   PRO B 660 "
           pdb=" CA  PRO B 660 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.72   40.28     0      5.00e+00 4.00e-02 6.49e+01
  dihedral pdb=" CA  ARG A 659 "
           pdb=" C   ARG A 659 "
           pdb=" N   PRO A 660 "
           pdb=" CA  PRO A 660 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.46   39.54     0      5.00e+00 4.00e-02 6.25e+01
  dihedral pdb=" CB  CYS A 161 "
           pdb=" SG  CYS A 161 "
           pdb=" SG  CYS A 172 "
           pdb=" CB  CYS A 172 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -117.90   31.90     1      1.00e+01 1.00e-02 1.45e+01
  ... (remaining 10301 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1304
       0.040 -    0.079: 285
       0.079 -    0.119: 96
       0.119 -    0.159: 11
       0.159 -    0.199: 2
  Chirality restraints: 1698
  Sorted by residual:
  chirality pdb=" C3' AMP A 901 "
            pdb=" C2' AMP A 901 "
            pdb=" C4' AMP A 901 "
            pdb=" O3' AMP A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.68    0.20 2.00e-01 2.50e+01 9.86e-01
  chirality pdb=" CA  PRO B 767 "
            pdb=" N   PRO B 767 "
            pdb=" C   PRO B 767 "
            pdb=" CB  PRO B 767 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 7.74e-01
  chirality pdb=" C2' AMP A 901 "
            pdb=" C1' AMP A 901 "
            pdb=" C3' AMP A 901 "
            pdb=" O2' AMP A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.60   -0.15 2.00e-01 2.50e+01 5.88e-01
  ... (remaining 1695 not shown)

  Planarity restraints: 3144
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 766 "    0.071 5.00e-02 4.00e+02   1.00e-01 1.61e+01
        pdb=" N   PRO B 767 "   -0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO B 767 "    0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B 767 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 766 "   -0.070 5.00e-02 4.00e+02   9.86e-02 1.56e+01
        pdb=" N   PRO A 767 "    0.170 5.00e-02 4.00e+02
        pdb=" CA  PRO A 767 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 767 "   -0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 659 "    0.047 5.00e-02 4.00e+02   7.11e-02 8.08e+00
        pdb=" N   PRO B 660 "   -0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO B 660 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 660 "    0.039 5.00e-02 4.00e+02
  ... (remaining 3141 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 1227
        2.19 -     2.79: 44475
        2.79 -     3.39: 62133
        3.39 -     4.00: 78625
        4.00 -     4.60: 123848
  Nonbonded interactions: 310308
  Sorted by model distance:
  nonbonded pdb=" O   PHE B 443 "
            pdb="HH11 ARG B 449 "
     model   vdw
     1.587 2.450
  nonbonded pdb=" OD1 ASP A  86 "
            pdb=" H   ASP A  87 "
     model   vdw
     1.591 2.450
  nonbonded pdb=" O   ALA B 150 "
            pdb=" HG1 THR B 154 "
     model   vdw
     1.606 2.450
  nonbonded pdb=" O   ALA A 150 "
            pdb=" HG1 THR A 154 "
     model   vdw
     1.613 2.450
  nonbonded pdb=" O   ILE A 264 "
            pdb=" HG1 THR A 268 "
     model   vdw
     1.617 2.450
  ... (remaining 310303 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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 individual isotropic
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:                  0.010
  Normalize map: mean=0, sd=1:             1.160
  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:             0.360
  Extract box with map and model:          0.770
  Check model and map are aligned:         0.170
  Set scattering table:                    0.200
  Process input model:                     45.130
  Find NCS groups from input model:        0.510
  Set up NCS constraints:                  0.060
  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:             0.010
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
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      :  0.004   0.148  11080  Z= 0.216
  Angle     :  0.623  10.618  15050  Z= 0.346
  Chirality :  0.039   0.199   1698
  Planarity :  0.005   0.100   1844
  Dihedral  : 14.099  89.892   3916
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.22), residues: 1348
  helix:  1.08 (0.17), residues: 832
  sheet: -0.65 (0.79), residues: 42
  loop : -1.06 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 166 
 HIS   0.004   0.001   HIS B 287 
 PHE   0.011   0.001   PHE B 377 
 TYR   0.019   0.001   TYR A 211 
 ARG   0.008   0.000   ARG B 416 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15284 (  658)
  hydrogen bonds       : angle       6.53742 ( 1944)
  SS BOND              : bond        0.00219 (    6)
  SS BOND              : angle       1.09383 (   12)
  covalent geometry    : bond        0.00446 (11074)
  covalent geometry    : angle       0.62218 (15038)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 MET cc_start: 0.8009 (mtt) cc_final: 0.7464 (mtt)
REVERT: A  423 PHE cc_start: 0.6180 (m-10) cc_final: 0.5974 (m-80)
REVERT: A  433 ILE cc_start: 0.8571 (mt) cc_final: 0.8345 (mt)
REVERT: A  574 TYR cc_start: 0.7604 (m-80) cc_final: 0.6989 (m-80)
REVERT: B  433 ILE cc_start: 0.8527 (mt) cc_final: 0.8306 (mt)
REVERT: B  574 TYR cc_start: 0.7635 (m-80) cc_final: 0.6995 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.5151
  time to fit residues: 105.5550
Evaluate side-chains
  110 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 114 optimal weight:    8.9990
   chunk 103 optimal weight:    0.8980
   chunk 57 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 55 optimal weight:    0.8980
   chunk 106 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 123 optimal weight:    2.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.215114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.162552 restraints weight = 31330.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.50
r_work: 0.3432 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.1173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  11080  Z= 0.198
  Angle     :  0.573   6.066  15050  Z= 0.301
  Chirality :  0.039   0.148   1698
  Planarity :  0.005   0.075   1844
  Dihedral  :  5.475  54.073   1494
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  5.11 %
    Favored  : 94.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  0.75 (0.22), residues: 1348
  helix:  1.49 (0.17), residues: 828
  sheet: -1.55 (0.77), residues: 42
  loop : -1.06 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 403 
 HIS   0.007   0.001   HIS B 287 
 PHE   0.015   0.001   PHE B 407 
 TYR   0.015   0.002   TYR A 343 
 ARG   0.005   0.001   ARG B 416 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04637 (  658)
  hydrogen bonds       : angle       4.83657 ( 1944)
  SS BOND              : bond        0.00451 (    6)
  SS BOND              : angle       1.08919 (   12)
  covalent geometry    : bond        0.00465 (11074)
  covalent geometry    : angle       0.57229 (15038)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 123
  time to evaluate  : 1.487 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 ILE cc_start: 0.8592 (mt) cc_final: 0.8345 (mt)
REVERT: B  209 MET cc_start: 0.7804 (tpp) cc_final: 0.7340 (tpt)
REVERT: B  423 PHE cc_start: 0.6325 (m-10) cc_final: 0.6074 (m-80)
REVERT: B  433 ILE cc_start: 0.8522 (mt) cc_final: 0.8312 (mt)
  outliers start: 3
  outliers final: 3
  residues processed: 125
  average time/residue: 0.5162
  time to fit residues: 90.8106
Evaluate side-chains
  122 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 119
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  607 ILE
Chi-restraints excluded: chain A residue  783 CYS
Chi-restraints excluded: chain B residue  323 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 87 optimal weight:    0.3980
   chunk 134 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   chunk 2 optimal weight:   20.0000
   chunk 24 optimal weight:    3.9990
   chunk 123 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 124 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.214571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.162345 restraints weight = 31329.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 2.52
r_work: 0.3442 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11080  Z= 0.143
  Angle     :  0.519   5.975  15050  Z= 0.264
  Chirality :  0.037   0.136   1698
  Planarity :  0.005   0.073   1844
  Dihedral  :  5.256  53.997   1494
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  6.60 %
    Favored  : 93.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  1.09 (0.23), residues: 1348
  helix:  1.73 (0.17), residues: 838
  sheet: -1.89 (0.79), residues: 42
  loop : -0.87 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 403 
 HIS   0.006   0.001   HIS B 287 
 PHE   0.013   0.001   PHE B 598 
 TYR   0.013   0.001   TYR A 343 
 ARG   0.005   0.000   ARG B 351 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04038 (  658)
  hydrogen bonds       : angle       4.45949 ( 1944)
  SS BOND              : bond        0.00306 (    6)
  SS BOND              : angle       0.92644 (   12)
  covalent geometry    : bond        0.00333 (11074)
  covalent geometry    : angle       0.51810 (15038)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 131
  time to evaluate  : 1.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 ILE cc_start: 0.8549 (mt) cc_final: 0.8318 (mt)
REVERT: B  433 ILE cc_start: 0.8534 (mt) cc_final: 0.8315 (mt)
  outliers start: 4
  outliers final: 3
  residues processed: 131
  average time/residue: 0.4904
  time to fit residues: 92.5891
Evaluate side-chains
  124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 121
  time to evaluate  : 1.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  658 MET
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  607 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 133 optimal weight:    0.8980
   chunk 28 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 132 optimal weight:    0.5980
   chunk 96 optimal weight:    6.9990
   chunk 44 optimal weight:    0.6980
   chunk 127 optimal weight:    0.0570
   chunk 78 optimal weight:    2.9990
   chunk 121 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.8500

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.214786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.162717 restraints weight = 31429.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 2.44
r_work: 0.3501 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3358 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11080  Z= 0.129
  Angle     :  0.509   5.807  15050  Z= 0.258
  Chirality :  0.036   0.133   1698
  Planarity :  0.005   0.073   1844
  Dihedral  :  5.139  54.522   1494
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  7.92 %
    Favored  : 91.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  1.28 (0.23), residues: 1348
  helix:  1.88 (0.17), residues: 840
  sheet: -1.80 (0.83), residues: 42
  loop : -0.80 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 403 
 HIS   0.004   0.001   HIS B 287 
 PHE   0.009   0.001   PHE B 407 
 TYR   0.012   0.001   TYR A 343 
 ARG   0.002   0.000   ARG B 449 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03732 (  658)
  hydrogen bonds       : angle       4.28986 ( 1944)
  SS BOND              : bond        0.00313 (    6)
  SS BOND              : angle       0.85339 (   12)
  covalent geometry    : bond        0.00299 (11074)
  covalent geometry    : angle       0.50855 (15038)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 121
  time to evaluate  : 1.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  433 ILE cc_start: 0.8576 (mt) cc_final: 0.8354 (mt)
REVERT: A  574 TYR cc_start: 0.7845 (m-80) cc_final: 0.7571 (m-80)
REVERT: B  433 ILE cc_start: 0.8550 (mt) cc_final: 0.8340 (mt)
  outliers start: 2
  outliers final: 2
  residues processed: 121
  average time/residue: 0.5542
  time to fit residues: 94.8061
Evaluate side-chains
  115 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 1.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  658 MET
Chi-restraints excluded: chain B residue  450 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 76 optimal weight:    0.6980
   chunk 130 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 114 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.207616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.155653 restraints weight = 31693.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.42
r_work: 0.3354 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068  11080  Z= 0.234
  Angle     :  0.598   6.556  15050  Z= 0.309
  Chirality :  0.039   0.149   1698
  Planarity :  0.005   0.076   1844
  Dihedral  :  5.525  59.248   1494
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  8.71 %
    Favored  : 90.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  0.82 (0.22), residues: 1348
  helix:  1.51 (0.17), residues: 830
  sheet: -1.69 (1.30), residues: 22
  loop : -1.01 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 403 
 HIS   0.009   0.001   HIS A 287 
 PHE   0.014   0.002   PHE B 706 
 TYR   0.015   0.002   TYR A 343 
 ARG   0.003   0.000   ARG A 588 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04281 (  658)
  hydrogen bonds       : angle       4.54476 ( 1944)
  SS BOND              : bond        0.00613 (    6)
  SS BOND              : angle       1.06298 (   12)
  covalent geometry    : bond        0.00561 (11074)
  covalent geometry    : angle       0.59752 (15038)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 1.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 TRP cc_start: 0.8046 (p-90) cc_final: 0.7757 (p90)
REVERT: A  683 MET cc_start: 0.4939 (ttt) cc_final: 0.4630 (ttm)
REVERT: B  433 ILE cc_start: 0.8508 (mt) cc_final: 0.8270 (mt)
  outliers start: 7
  outliers final: 6
  residues processed: 119
  average time/residue: 0.5297
  time to fit residues: 88.9296
Evaluate side-chains
  122 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 116
  time to evaluate  : 1.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  208 ILE
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  658 MET
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  607 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 3 optimal weight:   10.0000
   chunk 103 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 133 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 122 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.208550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.157698 restraints weight = 31473.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.22
r_work: 0.3387 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.2703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  11080  Z= 0.170
  Angle     :  0.543   5.866  15050  Z= 0.277
  Chirality :  0.037   0.136   1698
  Planarity :  0.005   0.076   1844
  Dihedral  :  5.355  57.299   1494
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  9.86 %
    Favored  : 89.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  1.00 (0.23), residues: 1348
  helix:  1.69 (0.17), residues: 828
  sheet: -1.94 (1.24), residues: 22
  loop : -0.98 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 403 
 HIS   0.005   0.001   HIS B 287 
 PHE   0.011   0.001   PHE B 598 
 TYR   0.014   0.001   TYR A 343 
 ARG   0.002   0.000   ARG B 416 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03904 (  658)
  hydrogen bonds       : angle       4.40041 ( 1944)
  SS BOND              : bond        0.00458 (    6)
  SS BOND              : angle       0.84584 (   12)
  covalent geometry    : bond        0.00397 (11074)
  covalent geometry    : angle       0.54278 (15038)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 118
  time to evaluate  : 1.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.6591 (mtpt) cc_final: 0.6082 (tttp)
REVERT: A  166 TRP cc_start: 0.7934 (p-90) cc_final: 0.7642 (p90)
REVERT: A  683 MET cc_start: 0.5195 (ttt) cc_final: 0.4881 (ttm)
REVERT: B  433 ILE cc_start: 0.8484 (mt) cc_final: 0.8245 (mt)
REVERT: B  570 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7604 (t)
  outliers start: 6
  outliers final: 5
  residues processed: 120
  average time/residue: 0.4856
  time to fit residues: 85.4993
Evaluate side-chains
  117 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 1.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  658 MET
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  570 THR
Chi-restraints excluded: chain B residue  607 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 70 optimal weight:    9.9990
   chunk 96 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 111 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 788 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.208087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.157082 restraints weight = 31627.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 2.41
r_work: 0.3369 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.2958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11080  Z= 0.157
  Angle     :  0.533   6.178  15050  Z= 0.270
  Chirality :  0.037   0.137   1698
  Planarity :  0.005   0.075   1844
  Dihedral  :  5.244  57.662   1494
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.95 %
    Favored  : 88.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  1.15 (0.23), residues: 1348
  helix:  1.80 (0.17), residues: 830
  sheet: -2.07 (1.19), residues: 22
  loop : -0.90 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 403 
 HIS   0.004   0.001   HIS B 287 
 PHE   0.010   0.001   PHE B 598 
 TYR   0.013   0.001   TYR A 343 
 ARG   0.002   0.000   ARG B 781 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03781 (  658)
  hydrogen bonds       : angle       4.30892 ( 1944)
  SS BOND              : bond        0.00402 (    6)
  SS BOND              : angle       0.90135 (   12)
  covalent geometry    : bond        0.00370 (11074)
  covalent geometry    : angle       0.53257 (15038)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 1.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.6656 (mtpt) cc_final: 0.6153 (tttp)
REVERT: A  166 TRP cc_start: 0.7917 (p-90) cc_final: 0.7699 (p90)
REVERT: A  167 TYR cc_start: 0.6569 (m-80) cc_final: 0.6320 (m-80)
REVERT: A  200 GLN cc_start: 0.7001 (pt0) cc_final: 0.6659 (pt0)
REVERT: A  402 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8030 (mp)
REVERT: A  570 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7785 (t)
REVERT: A  683 MET cc_start: 0.5610 (ttt) cc_final: 0.5172 (ttm)
REVERT: B  166 TRP cc_start: 0.8014 (p-90) cc_final: 0.7760 (p90)
REVERT: B  200 GLN cc_start: 0.6849 (pt0) cc_final: 0.6608 (pt0)
REVERT: B  402 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8071 (mp)
REVERT: B  570 THR cc_start: 0.7815 (OUTLIER) cc_final: 0.7582 (t)
  outliers start: 13
  outliers final: 8
  residues processed: 129
  average time/residue: 0.4956
  time to fit residues: 92.0657
Evaluate side-chains
  123 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 1.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  570 THR
Chi-restraints excluded: chain B residue  607 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 132 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 71 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 2 optimal weight:    9.9990
   chunk 62 optimal weight:    9.9990
   chunk 36 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.206376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.156393 restraints weight = 31641.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.33
r_work: 0.3356 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11080  Z= 0.169
  Angle     :  0.548   7.414  15050  Z= 0.278
  Chirality :  0.037   0.141   1698
  Planarity :  0.005   0.075   1844
  Dihedral  :  5.277  58.366   1494
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 10.30 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  1.09 (0.23), residues: 1348
  helix:  1.75 (0.17), residues: 830
  sheet: -2.16 (1.15), residues: 22
  loop : -0.93 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 403 
 HIS   0.005   0.001   HIS A 287 
 PHE   0.010   0.001   PHE B 598 
 TYR   0.013   0.001   TYR B 343 
 ARG   0.006   0.000   ARG B 416 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03852 (  658)
  hydrogen bonds       : angle       4.30787 ( 1944)
  SS BOND              : bond        0.00464 (    6)
  SS BOND              : angle       0.86682 (   12)
  covalent geometry    : bond        0.00398 (11074)
  covalent geometry    : angle       0.54723 (15038)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 1.576 
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   99 LYS cc_start: 0.6660 (mtpt) cc_final: 0.6130 (tttp)
REVERT: A  166 TRP cc_start: 0.7909 (p-90) cc_final: 0.7659 (p90)
REVERT: A  200 GLN cc_start: 0.7203 (pt0) cc_final: 0.6857 (pt0)
REVERT: A  570 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7797 (t)
REVERT: A  683 MET cc_start: 0.5467 (ttt) cc_final: 0.5043 (ttm)
REVERT: B  166 TRP cc_start: 0.7933 (p-90) cc_final: 0.7650 (p90)
REVERT: B  200 GLN cc_start: 0.6964 (pt0) cc_final: 0.6703 (pt0)
REVERT: B  402 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8080 (mp)
REVERT: B  570 THR cc_start: 0.7787 (OUTLIER) cc_final: 0.7560 (t)
  outliers start: 15
  outliers final: 11
  residues processed: 122
  average time/residue: 0.4539
  time to fit residues: 82.5337
Evaluate side-chains
  125 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 1.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  658 MET
Chi-restraints excluded: chain A residue  783 CYS
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  570 THR
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  607 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 126 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 71 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 97 optimal weight:    0.0980
   chunk 29 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.206746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.156952 restraints weight = 31546.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 2.29
r_work: 0.3367 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.3290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11080  Z= 0.147
  Angle     :  0.528   6.286  15050  Z= 0.267
  Chirality :  0.036   0.136   1698
  Planarity :  0.005   0.074   1844
  Dihedral  :  5.199  57.254   1494
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 10.12 %
    Favored  : 88.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  1.22 (0.23), residues: 1348
  helix:  1.87 (0.17), residues: 830
  sheet: -2.20 (1.14), residues: 22
  loop : -0.90 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 403 
 HIS   0.003   0.001   HIS B 287 
 PHE   0.009   0.001   PHE B 598 
 TYR   0.013   0.001   TYR A 343 
 ARG   0.010   0.000   ARG B 416 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03720 (  658)
  hydrogen bonds       : angle       4.25710 ( 1944)
  SS BOND              : bond        0.00395 (    6)
  SS BOND              : angle       0.87088 (   12)
  covalent geometry    : bond        0.00344 (11074)
  covalent geometry    : angle       0.52797 (15038)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 1.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 TRP cc_start: 0.7878 (p-90) cc_final: 0.7659 (p90)
REVERT: A  200 GLN cc_start: 0.7255 (pt0) cc_final: 0.6909 (pt0)
REVERT: A  402 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8027 (mp)
REVERT: A  570 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7833 (t)
REVERT: A  683 MET cc_start: 0.5552 (ttt) cc_final: 0.5218 (ttm)
REVERT: B   99 LYS cc_start: 0.6674 (mtpt) cc_final: 0.6150 (tttp)
REVERT: B  166 TRP cc_start: 0.7913 (p-90) cc_final: 0.7616 (p90)
REVERT: B  200 GLN cc_start: 0.6974 (pt0) cc_final: 0.6668 (pt0)
REVERT: B  402 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8056 (mp)
REVERT: B  570 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7553 (t)
REVERT: B  574 TYR cc_start: 0.7987 (m-80) cc_final: 0.7605 (m-80)
  outliers start: 14
  outliers final: 8
  residues processed: 129
  average time/residue: 0.4921
  time to fit residues: 94.1964
Evaluate side-chains
  125 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  570 THR
Chi-restraints excluded: chain B residue  607 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 112 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 107 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 117 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 123 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.206609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.156181 restraints weight = 31787.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.24
r_work: 0.3359 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3224 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  11080  Z= 0.157
  Angle     :  0.542   6.733  15050  Z= 0.273
  Chirality :  0.037   0.138   1698
  Planarity :  0.005   0.075   1844
  Dihedral  :  5.217  57.606   1494
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 10.12 %
    Favored  : 88.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  1.19 (0.23), residues: 1348
  helix:  1.84 (0.17), residues: 830
  sheet: -2.25 (1.13), residues: 22
  loop : -0.91 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 403 
 HIS   0.004   0.001   HIS B 287 
 PHE   0.010   0.001   PHE B 598 
 TYR   0.013   0.001   TYR B 343 
 ARG   0.008   0.000   ARG B 416 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03760 (  658)
  hydrogen bonds       : angle       4.28184 ( 1944)
  SS BOND              : bond        0.00425 (    6)
  SS BOND              : angle       0.89984 (   12)
  covalent geometry    : bond        0.00369 (11074)
  covalent geometry    : angle       0.54201 (15038)

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

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

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2696 Ramachandran restraints generated.
    1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 1.655 
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  166 TRP cc_start: 0.7928 (p-90) cc_final: 0.7655 (p90)
REVERT: A  200 GLN cc_start: 0.7265 (pt0) cc_final: 0.6959 (pt0)
REVERT: A  402 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8044 (mp)
REVERT: A  570 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7877 (t)
REVERT: A  576 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8077 (ttp)
REVERT: A  683 MET cc_start: 0.5642 (ttt) cc_final: 0.5236 (ttm)
REVERT: A  787 HIS cc_start: 0.6360 (t-90) cc_final: 0.6091 (t-90)
REVERT: B  166 TRP cc_start: 0.7958 (p-90) cc_final: 0.7678 (p90)
REVERT: B  200 GLN cc_start: 0.6973 (pt0) cc_final: 0.6647 (pt0)
REVERT: B  402 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8073 (mp)
REVERT: B  570 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.7569 (t)
REVERT: B  574 TYR cc_start: 0.8004 (m-80) cc_final: 0.7654 (m-80)
  outliers start: 14
  outliers final: 9
  residues processed: 132
  average time/residue: 0.4549
  time to fit residues: 89.1436
Evaluate side-chains
  132 residues out of total 1136 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 1.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  576 MET
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain B residue  323 SER
Chi-restraints excluded: chain B residue  402 LEU
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  522 VAL
Chi-restraints excluded: chain B residue  570 THR
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  607 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 2 optimal weight:   20.0000
   chunk 41 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 67 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 85 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   chunk 62 optimal weight:    8.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.207438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.157290 restraints weight = 31722.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.29
r_work: 0.3365 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11080  Z= 0.135
  Angle     :  0.528   6.639  15050  Z= 0.266
  Chirality :  0.036   0.138   1698
  Planarity :  0.005   0.075   1844
  Dihedral  :  5.154  56.757   1494
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 10.39 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.57 %
    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:  1.29 (0.23), residues: 1348
  helix:  1.96 (0.17), residues: 830
  sheet: -2.36 (1.11), residues: 22
  loop : -0.91 (0.28), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 403 
 HIS   0.003   0.001   HIS B 633 
 PHE   0.009   0.001   PHE B 598 
 TYR   0.012   0.001   TYR A 343 
 ARG   0.009   0.000   ARG B 416 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  658)
  hydrogen bonds       : angle       4.23678 ( 1944)
  SS BOND              : bond        0.00354 (    6)
  SS BOND              : angle       0.86568 (   12)
  covalent geometry    : bond        0.00313 (11074)
  covalent geometry    : angle       0.52783 (15038)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10879.15 seconds
wall clock time: 186 minutes 56.52 seconds (11216.52 seconds total)