Starting phenix.real_space_refine
on Fri Oct 23 13:14:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/22dz_68190/10_2026/22dz_68190.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/22dz_68190/10_2026/22dz_68190.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/22dz_68190/10_2026/22dz_68190.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/22dz_68190/10_2026/22dz_68190.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/22dz_68190/10_2026/22dz_68190.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/22dz_68190/10_2026/22dz_68190.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.030
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: 4
    Type Number    sf(0)   Gaussians
     S      65      5.16       5
     C    6154      2.51       5
     N    1615      2.21       5
     O    1896      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9730
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "H"
      Number of atoms: 857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 857
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 1, 'TRANS': 109}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 2828
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2828
          Classifications: {'peptide': 366}
          Link IDs: {'PTRANS': 17, 'TRANS': 348}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 6045
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 773, 6045
          Classifications: {'peptide': 773}
          Link IDs: {'PTRANS': 32, 'TRANS': 740}
          Chain breaks: 5
  Time building chain proxies: 1.90, per 1000 atoms: 0.20
  Number of scatterers: 9730
  At special positions: 0
  Unit cell: (116.5, 127.684, 122.092, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      65     16.00
     O    1896      8.00
     N    1615      7.00
     C    6154      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=24, symmetry=0
    Simple disulfide: pdb=" SG  CYS H 806 " - pdb=" SG  CYS H 828 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 811 " - pdb=" SG  CYS H 817 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 912 " - pdb=" SG  CYS H 925 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 339 " - pdb=" SG  CYS F 349 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 383 " - pdb=" SG  CYS F 407 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 425 " - pdb=" SG  CYS F 478 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 437 " - pdb=" SG  CYS F 585 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 503 " - pdb=" SG  CYS F 526 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 603 " - pdb=" SG  CYS F 654 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 620 " - pdb=" SG  CYS F 650 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 679 " - pdb=" SG  CYS F 713 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  30 " - pdb=" SG  CYS C 195 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 176 " - pdb=" SG  CYS C 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 185 " - pdb=" SG  CYS C 237 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 339 " - pdb=" SG  CYS C 349 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 383 " - pdb=" SG  CYS C 407 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 425 " - pdb=" SG  CYS C 478 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 437 " - pdb=" SG  CYS C 585 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 503 " - pdb=" SG  CYS C 526 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 603 " - pdb=" SG  CYS C 654 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 620 " - pdb=" SG  CYS C 650 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 806 " - pdb=" SG  CYS C 828 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 811 " - pdb=" SG  CYS C 817 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 912 " - pdb=" SG  CYS C 925 " 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: 0.82
  Conformation dependent library (CDL) restraints added in 264.4 milliseconds
  

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2334

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 21 sheets defined
      20.6% alpha, 15.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'H' and resid 805 through 811
      removed outlier: 3.654A  pdb=" N   VAL H 810 " --> pdb=" O   CYS H 806 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 814 through 825
      removed outlier: 3.646A  pdb=" N   GLU H 818 " --> pdb=" O   PHE H 814 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 828 through 834
    Processing helix  chain 'H' and resid 910 through 915
      removed outlier: 3.762A  pdb=" N   GLN H 915 " --> pdb=" O   CYS H 912 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 926 through 931
    Processing helix  chain 'H' and resid 1032 through 1038
    Processing helix  chain 'H' and resid 1050 through 1058
      removed outlier: 3.673A  pdb=" N   ILE H1054 " --> pdb=" O   SER H1050 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 1059 through 1084
      removed outlier: 4.183A  pdb=" N   ASP H1064 " --> pdb=" O   VAL H1060 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   ALA H1065 " --> pdb=" O   LEU H1061 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ARG H1069 " --> pdb=" O   ALA H1065 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LEU H1070 " --> pdb=" O   GLN H1066 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU H1078 " --> pdb=" O   ARG H1074 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   ASN H1079 " --> pdb=" O   LEU H1075 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ALA H1080 " --> pdb=" O   THR H1076 " (cutoff:3.500A)
      removed outlier: 5.420A  pdb=" N   PHE H1081 " --> pdb=" O   THR H1077 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 345 through 352
    Processing helix  chain 'F' and resid 385 through 390
      removed outlier: 3.548A  pdb=" N   SER F 390 " --> pdb=" O   SER F 386 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 410 through 415
    Processing helix  chain 'F' and resid 678 through 682
      removed outlier: 3.728A  pdb=" N   HIS F 681 " --> pdb=" O   ALA F 678 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ILE F 682 " --> pdb=" O   CYS F 679 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 678 through 682'
    Processing helix  chain 'F' and resid 693 through 699
      removed outlier: 3.919A  pdb=" N   ARG F 699 " --> pdb=" O   SER F 695 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 41
      removed outlier: 3.696A  pdb=" N   PHE C  40 " --> pdb=" O   GLN C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 49 through 53
      removed outlier: 3.512A  pdb=" N   LYS C  52 " --> pdb=" O   ASP C  49 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 231
      removed outlier: 3.702A  pdb=" N   TYR C 231 " --> pdb=" O   SER C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 345 through 352
    Processing helix  chain 'C' and resid 386 through 390
      removed outlier: 3.537A  pdb=" N   SER C 390 " --> pdb=" O   PRO C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 410 through 415
    Processing helix  chain 'C' and resid 429 through 433
      removed outlier: 3.556A  pdb=" N   ALA C 432 " --> pdb=" O   SER C 429 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ILE C 433 " --> pdb=" O   PRO C 430 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 429 through 433'
    Processing helix  chain 'C' and resid 451 through 456
      removed outlier: 4.528A  pdb=" N   SER C 454 " --> pdb=" O   SER C 451 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU C 456 " --> pdb=" O   LYS C 453 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 595 through 599
      removed outlier: 3.761A  pdb=" N   GLN C 599 " --> pdb=" O   ILE C 596 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 693 through 698
    Processing helix  chain 'C' and resid 814 through 822
      removed outlier: 3.776A  pdb=" N   LEU C 820 " --> pdb=" O   LYS C 816 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 826 through 836
    Processing helix  chain 'C' and resid 908 through 913
      removed outlier: 3.732A  pdb=" N   MET C 913 " --> pdb=" O   TYR C 909 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 914 through 915
      No H-bonds generated for 'chain 'C' and resid 914 through 915'
    Processing helix  chain 'C' and resid 916 through 920
      removed outlier: 3.601A  pdb=" N   ALA C 920 " --> pdb=" O   PRO C 917 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 926 through 931
    Processing helix  chain 'C' and resid 1032 through 1040
      removed outlier: 3.688A  pdb=" N   LEU C1036 " --> pdb=" O   ALA C1032 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA C1037 " --> pdb=" O   LEU C1033 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LEU C1040 " --> pdb=" O   LEU C1036 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1050 through 1058
    Processing helix  chain 'C' and resid 1059 through 1085
      removed outlier: 4.150A  pdb=" N   ASP C1064 " --> pdb=" O   VAL C1060 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   ALA C1065 " --> pdb=" O   LEU C1061 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLN C1066 " --> pdb=" O   GLU C1062 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG C1069 " --> pdb=" O   ALA C1065 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   THR C1077 " --> pdb=" O   GLY C1073 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 361 through 363
      removed outlier: 3.674A  pdb=" N   VAL F 363 " --> pdb=" O   VAL F 659 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   VAL F 659 " --> pdb=" O   VAL F 363 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   THR F 672 " --> pdb=" O   LEU F 715 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 373 through 376
      removed outlier: 3.538A  pdb=" N   VAL F 604 " --> pdb=" O   GLY F 615 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL F 611 " --> pdb=" O   LEU F 608 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'F' and resid 400 through 404
      removed outlier: 3.695A  pdb=" N   LYS F 400 " --> pdb=" O   TYR F 445 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   TYR F 445 " --> pdb=" O   LYS F 400 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   SER F 440 " --> pdb=" O   GLN F 576 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN F 576 " --> pdb=" O   SER F 440 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 499 through 500
      removed outlier: 3.691A  pdb=" N   TYR F 499 " --> pdb=" O   SER F 559 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER F 559 " --> pdb=" O   TYR F 499 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 513 through 514
    Processing sheet with id=AA6, first strand: chain 'F' and resid 631 through 632
      removed outlier: 3.671A  pdb=" N   TYR F 641 " --> pdb=" O   TYR F 649 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 33 through 36
    Processing sheet with id=AA8, first strand: chain 'C' and resid 68 through 69
    Processing sheet with id=AA9, first strand: chain 'C' and resid 72 through 76
      removed outlier: 3.787A  pdb=" N   GLY C  73 " --> pdb=" O   LEU C 321 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU C 321 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE C  75 " --> pdb=" O   GLN C 319 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   PHE C 313 " --> pdb=" O   TYR C  85 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 76
      removed outlier: 3.787A  pdb=" N   GLY C  73 " --> pdb=" O   LEU C 321 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU C 321 " --> pdb=" O   GLY C  73 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE C  75 " --> pdb=" O   GLN C 319 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   GLY C 115 " --> pdb=" O   LEU C 318 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   PHE C 116 " --> pdb=" O   ILE C 256 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   VAL C 263 " --> pdb=" O   THR C 283 " (cutoff:3.500A)
      removed outlier: 4.611A  pdb=" N   THR C 283 " --> pdb=" O   VAL C 263 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   LEU C 265 " --> pdb=" O   PHE C 281 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 110 through 111
      removed outlier: 4.644A  pdb=" N   ALA C 146 " --> pdb=" O   ILE C 296 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   ARG C 235 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLU C 188 " --> pdb=" O   ASN C 233 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 110 through 111
      removed outlier: 4.644A  pdb=" N   ALA C 146 " --> pdb=" O   ILE C 296 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 126 through 129
      removed outlier: 4.239A  pdb=" N   SER C 126 " --> pdb=" O   ILE C 140 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ALA C 309 " --> pdb=" O   THR C 139 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 153 through 155
    Processing sheet with id=AB6, first strand: chain 'C' and resid 206 through 208
    Processing sheet with id=AB7, first strand: chain 'C' and resid 420 through 422
    Processing sheet with id=AB8, first strand: chain 'C' and resid 440 through 442
      removed outlier: 3.787A  pdb=" N   SER C 440 " --> pdb=" O   GLN C 576 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLN C 576 " --> pdb=" O   SER C 440 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   THR C 574 " --> pdb=" O   ILE C 442 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 513 through 514
      removed outlier: 3.645A  pdb=" N   VAL C 514 " --> pdb=" O   ARG C 505 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   TRP C 553 " --> pdb=" O   PHE C 506 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   LYS C 543 " --> pdb=" O   LEU C 554 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 604 through 608
      removed outlier: 3.727A  pdb=" N   VAL C 604 " --> pdb=" O   GLY C 615 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLY C 615 " --> pdb=" O   VAL C 604 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLY C 613 " --> pdb=" O   TYR C 606 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 641 through 642
    Processing sheet with id=AC3, first strand: chain 'C' and resid 803 through 804

    219 hydrogen bonds defined for protein.
    570 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.61

  Time building geometry restraints manager: 1.12 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3146
        1.34 -     1.46: 2453
        1.46 -     1.58: 4257
        1.58 -     1.70: 0
        1.70 -     1.82: 82
  Bond restraints: 9938
  Sorted by residual:
  bond pdb=" N   GLU C 536 "
       pdb=" CA  GLU C 536 "
    ideal  model  delta    sigma   weight residual
    1.457  1.483 -0.026 1.29e-02 6.01e+03 3.91e+00
  bond pdb=" C   SER C 524 "
       pdb=" N   PRO C 525 "
    ideal  model  delta    sigma   weight residual
    1.331  1.347 -0.015 7.90e-03 1.60e+04 3.72e+00
  bond pdb=" N   VAL C 530 "
       pdb=" CA  VAL C 530 "
    ideal  model  delta    sigma   weight residual
    1.461  1.479 -0.018 1.23e-02 6.61e+03 2.16e+00
  bond pdb=" CA  TRP C 535 "
       pdb=" C   TRP C 535 "
    ideal  model  delta    sigma   weight residual
    1.523  1.504  0.019 1.34e-02 5.57e+03 1.96e+00
  bond pdb=" CA  VAL C 530 "
       pdb=" CB  VAL C 530 "
    ideal  model  delta    sigma   weight residual
    1.537  1.554 -0.017 1.29e-02 6.01e+03 1.76e+00
  ... (remaining 9933 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 12926
        1.39 -     2.78: 467
        2.78 -     4.18: 75
        4.18 -     5.57: 13
        5.57 -     6.96: 4
  Bond angle restraints: 13485
  Sorted by residual:
  angle pdb=" N   SER C 528 "
        pdb=" CA  SER C 528 "
        pdb=" C   SER C 528 "
      ideal   model   delta    sigma   weight residual
     111.40  105.97    5.43 1.22e+00 6.72e-01 1.98e+01
  angle pdb=" N   SER C1041 "
        pdb=" CA  SER C1041 "
        pdb=" C   SER C1041 "
      ideal   model   delta    sigma   weight residual
     114.75  110.05    4.70 1.26e+00 6.30e-01 1.39e+01
  angle pdb=" N   LEU H1078 "
        pdb=" CA  LEU H1078 "
        pdb=" C   LEU H1078 "
      ideal   model   delta    sigma   weight residual
     114.62  110.43    4.19 1.14e+00 7.69e-01 1.35e+01
  angle pdb=" N   THR C 533 "
        pdb=" CA  THR C 533 "
        pdb=" C   THR C 533 "
      ideal   model   delta    sigma   weight residual
     108.23  101.91    6.32 1.72e+00 3.38e-01 1.35e+01
  angle pdb=" N   SER F 598 "
        pdb=" CA  SER F 598 "
        pdb=" C   SER F 598 "
      ideal   model   delta    sigma   weight residual
     114.56  110.24    4.32 1.27e+00 6.20e-01 1.16e+01
  ... (remaining 13480 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 5666
       17.79 -    35.57: 235
       35.57 -    53.36: 51
       53.36 -    71.14: 9
       71.14 -    88.93: 2
  Dihedral angle restraints: 5963
    sinusoidal: 2312
      harmonic: 3651
  Sorted by residual:
  dihedral pdb=" N   GLU C 536 "
           pdb=" C   GLU C 536 "
           pdb=" CA  GLU C 536 "
           pdb=" CB  GLU C 536 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.41   -8.61     0      2.50e+00 1.60e-01 1.19e+01
  dihedral pdb=" CA  ASP C 272 "
           pdb=" CB  ASP C 272 "
           pdb=" CG  ASP C 272 "
           pdb=" OD1 ASP C 272 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.34   59.34     1      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" CA  PRO F 463 "
           pdb=" C   PRO F 463 "
           pdb=" N   ILE F 464 "
           pdb=" CA  ILE F 464 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.10  -16.90     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 5960 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1318
       0.059 -    0.117: 168
       0.117 -    0.176: 8
       0.176 -    0.234: 5
       0.234 -    0.293: 1
  Chirality restraints: 1500
  Sorted by residual:
  chirality pdb=" CA  GLU C 536 "
            pdb=" N   GLU C 536 "
            pdb=" C   GLU C 536 "
            pdb=" CB  GLU C 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.14e+00
  chirality pdb=" CA  TRP C 535 "
            pdb=" N   TRP C 535 "
            pdb=" C   TRP C 535 "
            pdb=" CB  TRP C 535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.32e-01
  chirality pdb=" CA  VAL C 375 "
            pdb=" N   VAL C 375 "
            pdb=" C   VAL C 375 "
            pdb=" CB  VAL C 375 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.27e-01
  ... (remaining 1497 not shown)

  Planarity restraints: 1744
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY F 462 "   -0.046 5.00e-02 4.00e+02   7.02e-02 7.89e+00
        pdb=" N   PRO F 463 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO F 463 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO F 463 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 195 "    0.019 5.00e-02 4.00e+02   2.89e-02 1.34e+00
        pdb=" N   PRO C 196 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO C 196 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C 196 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 133 "    0.018 5.00e-02 4.00e+02   2.72e-02 1.18e+00
        pdb=" N   PRO C 134 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO C 134 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO C 134 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1741 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2373
        2.79 -     3.31: 8667
        3.31 -     3.84: 15674
        3.84 -     4.37: 18115
        4.37 -     4.90: 31065
  Nonbonded interactions: 75894
  Sorted by model distance:
  nonbonded pdb=" O   ILE F 433 "
            pdb=" OH  TYR F 438 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OH  TYR H 824 "
            pdb=" OD1 ASP H1068 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OH  TYR C 448 "
            pdb=" O   MET C 452 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   SER C1038 "
            pdb=" OG  SER C1041 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   ASN H1072 "
            pdb=" OG1 THR H1076 "
     model   vdw
     2.288 3.040
  ... (remaining 75889 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: 0.00
========== 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 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:                  0.000
  Normalize map: mean=0, sd=1:             4.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.270
  Find NCS groups from input model:        0.040
  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:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6299
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      :  0.002   0.041   9962  Z= 0.139
  Angle     :  0.606   6.962  13533  Z= 0.386
  Chirality :  0.040   0.293   1500
  Planarity :  0.003   0.070   1744
  Dihedral  :  9.820  88.928   3557
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.61 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  :  7.81 %
    Favored  : 87.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.28 (0.20), residues: 1222
  helix: -2.62 (0.30), residues: 195
  sheet: -2.87 (0.34), residues: 189
  loop : -3.10 (0.18), residues: 838

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 141 
 TYR   0.005   0.001   TYR F 397 
 PHE   0.006   0.001   PHE H1044 
 TRP   0.006   0.001   TRP C 535 
 HIS   0.001   0.000   HIS C 681 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00215 /  0.14 ( 9938)
  covalent geometry    : angle       0.60604 /  0.39 (13485)
  SS BOND              : bond        0.00193 /  0.14 (   24)
  SS BOND              : angle       0.51513 /  0.35 (   48)
  hydrogen bonds       : bond        0.25926 / 16.11 (  201)
  hydrogen bonds       : angle       9.93775 /  6.92 (  570)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 215
  time to evaluate  : 0.255 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  816 LYS cc_start: 0.8623 (mmtp) cc_final: 0.8341 (tppp)
REVERT: F  346 GLN cc_start: 0.7500 (mt0) cc_final: 0.7222 (mp10)
REVERT: F  495 LEU cc_start: 0.8458 (mp) cc_final: 0.8229 (mt)
REVERT: F  506 PHE cc_start: 0.7674 (OUTLIER) cc_final: 0.6465 (t80)
REVERT: F  529 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7863 (tt)
REVERT: F  540 TYR cc_start: 0.8379 (t80) cc_final: 0.8170 (t80)
REVERT: F  563 MET cc_start: 0.5605 (tpt) cc_final: 0.5357 (mmm)
REVERT: F  696 MET cc_start: -0.0583 (mmt) cc_final: -0.1353 (mpp)
REVERT: C  220 ASN cc_start: 0.7463 (t0) cc_final: 0.6941 (t0)
REVERT: C  399 PHE cc_start: 0.4078 (p90) cc_final: 0.3594 (p90)
REVERT: C  523 TYR cc_start: 0.6695 (OUTLIER) cc_final: 0.4219 (m-80)
REVERT: C  686 MET cc_start: 0.1512 (mtt) cc_final: 0.1222 (mtm)
  outliers start: 54
  outliers final: 14
  residues processed: 257
  average time/residue: 0.1087
  time to fit residues: 37.7398
Evaluate side-chains
  138 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  814 PHE
Chi-restraints excluded: chain H residue 1056 GLN
Chi-restraints excluded: chain F residue  381 VAL
Chi-restraints excluded: chain F residue  438 TYR
Chi-restraints excluded: chain F residue  506 PHE
Chi-restraints excluded: chain F residue  529 ILE
Chi-restraints excluded: chain F residue  596 ILE
Chi-restraints excluded: chain F residue  697 LEU
Chi-restraints excluded: chain C residue  101 PHE
Chi-restraints excluded: chain C residue  377 GLN
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain C residue  506 PHE
Chi-restraints excluded: chain C residue  523 TYR
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  540 TYR
Chi-restraints excluded: chain C residue  564 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51]
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.0270
   chunk 113 optimal weight:    0.0970
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 123 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.8238

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 915 GLN
H1031 GLN
H1042 ASN
F 406 ASN
F 410 ASN
F 421 ASN
F 427 GLN
F 466 GLN
F 566 GLN
F 582 ASN
F 599 GLN
F 628 GLN
F 681 HIS
C  37 GLN
C  98 GLN
C 104 ASN
C 277 ASN
C 280 GLN
C 319 GLN
C 421 ASN
C 501 ASN
C 522 GLN
C 566 GLN
C 576 GLN
C 592 ASN
C 627 GLN
C 808 GLN
C1084 GLN

Total number of N/Q/H flips: 28

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.133750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.111580 restraints weight = 41695.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.4223 rms_B_bonded: 5.83
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9962  Z= 0.133
  Angle     :  0.619  11.405  13533  Z= 0.316
  Chirality :  0.043   0.319   1500
  Planarity :  0.004   0.067   1744
  Dihedral  :  6.315  86.493   1395
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.59 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 13.31 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.52 (0.21), residues: 1222
  helix: -1.57 (0.34), residues: 205
  sheet: -2.37 (0.36), residues: 173
  loop : -2.71 (0.19), residues: 844

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H1057 
 TYR   0.014   0.001   TYR C 577 
 PHE   0.013   0.001   PHE C 313 
 TRP   0.014   0.001   TRP F 553 
 HIS   0.002   0.001   HIS C 194 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 ( 9938)
  covalent geometry    : angle       0.61749 /  0.32 (13485)
  SS BOND              : bond        0.00211 /  0.12 (   24)
  SS BOND              : angle       1.03671 /  0.59 (   48)
  hydrogen bonds       : bond        0.04395 /  2.74 (  201)
  hydrogen bonds       : angle       6.53104 /  4.56 (  570)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 138
  time to evaluate  : 0.381 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  529 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7891 (tt)
REVERT: F  540 TYR cc_start: 0.8796 (t80) cc_final: 0.8463 (t80)
REVERT: F  683 SER cc_start: 0.7450 (m) cc_final: 0.7220 (p)
REVERT: F  696 MET cc_start: -0.0344 (mmt) cc_final: -0.0750 (mpp)
REVERT: C   77 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6735 (t80)
REVERT: C  399 PHE cc_start: 0.4505 (p90) cc_final: 0.4105 (p90)
REVERT: C  479 LEU cc_start: 0.8586 (tt) cc_final: 0.8280 (mm)
REVERT: C  569 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6311 (mtt)
REVERT: C  686 MET cc_start: 0.1222 (mtt) cc_final: 0.1016 (mtm)
REVERT: C 1075 LEU cc_start: 0.6429 (pp) cc_final: 0.6165 (pp)
  outliers start: 37
  outliers final: 20
  residues processed: 168
  average time/residue: 0.0932
  time to fit residues: 22.2175
Evaluate side-chains
  141 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  929 VAL
Chi-restraints excluded: chain H residue 1056 GLN
Chi-restraints excluded: chain F residue  373 SER
Chi-restraints excluded: chain F residue  381 VAL
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  438 TYR
Chi-restraints excluded: chain F residue  450 LEU
Chi-restraints excluded: chain F residue  526 CYS
Chi-restraints excluded: chain F residue  529 ILE
Chi-restraints excluded: chain F residue  596 ILE
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   77 TYR
Chi-restraints excluded: chain C residue  274 TYR
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain C residue  470 LYS
Chi-restraints excluded: chain C residue  506 PHE
Chi-restraints excluded: chain C residue  523 TYR
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  540 TYR
Chi-restraints excluded: chain C residue  564 THR
Chi-restraints excluded: chain C residue  569 MET
Chi-restraints excluded: chain C residue  577 TYR
Chi-restraints excluded: chain C residue 1042 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [24, 35, 101, 106, 10, 27, 115, 104, 78, 89, 108]
   chunk 24 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 101 optimal weight:    6.9990
   chunk 106 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 27 optimal weight:    5.9990
   chunk 115 optimal weight:    6.9990
   chunk 104 optimal weight:    5.9990
   chunk 78 optimal weight:    4.9990
   chunk 89 optimal weight:    0.7980
   chunk 108 optimal weight:    7.9990
   overall best weight:    2.1386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 815 GLN
F 681 HIS
C  91 HIS
C 222 ASN
** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 582 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.126765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.103688 restraints weight = 39717.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.4106 rms_B_bonded: 5.80
r_work (final): 0.4106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.4488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9962  Z= 0.232
  Angle     :  0.714   8.581  13533  Z= 0.371
  Chirality :  0.046   0.319   1500
  Planarity :  0.005   0.055   1744
  Dihedral  :  6.085  84.579   1383
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 15.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.82 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 14.42 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.42 (0.22), residues: 1222
  helix: -1.47 (0.33), residues: 229
  sheet: -2.05 (0.35), residues: 198
  loop : -2.73 (0.20), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 141 
 TYR   0.022   0.002   TYR C 909 
 PHE   0.018   0.002   PHE F 366 
 TRP   0.008   0.002   TRP F 553 
 HIS   0.005   0.001   HIS C 194 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00507 /  0.23 ( 9938)
  covalent geometry    : angle       0.71185 /  0.37 (13485)
  SS BOND              : bond        0.00387 /  0.24 (   24)
  SS BOND              : angle       1.12887 /  0.71 (   48)
  hydrogen bonds       : bond        0.04366 /  2.64 (  201)
  hydrogen bonds       : angle       6.51471 /  4.43 (  570)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 117
  time to evaluate  : 0.324 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  433 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7962 (pt)
REVERT: F  464 ILE cc_start: 0.8227 (mm) cc_final: 0.7773 (tt)
REVERT: F  529 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7921 (tt)
REVERT: F  540 TYR cc_start: 0.8817 (t80) cc_final: 0.8482 (t80)
REVERT: F  605 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7529 (mm-30)
REVERT: F  696 MET cc_start: 0.1578 (mmt) cc_final: 0.1116 (ttm)
REVERT: C   77 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.6267 (t80)
REVERT: C  399 PHE cc_start: 0.5521 (p90) cc_final: 0.4843 (p90)
REVERT: C  502 LYS cc_start: 0.7544 (tttt) cc_final: 0.7005 (tptt)
REVERT: C  571 PHE cc_start: 0.7980 (p90) cc_final: 0.7691 (p90)
REVERT: C  612 SER cc_start: 0.7633 (p) cc_final: 0.7253 (t)
REVERT: C  686 MET cc_start: 0.1555 (mtt) cc_final: 0.1091 (mtm)
REVERT: C 1056 GLN cc_start: 0.8680 (tp40) cc_final: 0.8362 (tp40)
REVERT: C 1075 LEU cc_start: 0.6595 (pp) cc_final: 0.6335 (pp)
  outliers start: 48
  outliers final: 27
  residues processed: 155
  average time/residue: 0.0986
  time to fit residues: 21.2802
Evaluate side-chains
  134 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  929 VAL
Chi-restraints excluded: chain H residue 1042 ASN
Chi-restraints excluded: chain H residue 1053 ASP
Chi-restraints excluded: chain H residue 1060 VAL
Chi-restraints excluded: chain H residue 1061 LEU
Chi-restraints excluded: chain F residue  373 SER
Chi-restraints excluded: chain F residue  375 VAL
Chi-restraints excluded: chain F residue  381 VAL
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  433 ILE
Chi-restraints excluded: chain F residue  438 TYR
Chi-restraints excluded: chain F residue  450 LEU
Chi-restraints excluded: chain F residue  505 ARG
Chi-restraints excluded: chain F residue  529 ILE
Chi-restraints excluded: chain F residue  596 ILE
Chi-restraints excluded: chain F residue  697 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   77 TYR
Chi-restraints excluded: chain C residue  245 ILE
Chi-restraints excluded: chain C residue  274 TYR
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain C residue  470 LYS
Chi-restraints excluded: chain C residue  506 PHE
Chi-restraints excluded: chain C residue  523 TYR
Chi-restraints excluded: chain C residue  564 THR
Chi-restraints excluded: chain C residue  567 LEU
Chi-restraints excluded: chain C residue  577 TYR
Chi-restraints excluded: chain C residue  623 VAL
Chi-restraints excluded: chain C residue 1061 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [25, 9, 48, 22, 74, 82, 16, 108, 64, 110, 103]
   chunk 25 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 74 optimal weight:    0.0010
   chunk 82 optimal weight:    0.0670
   chunk 16 optimal weight:    0.9980
   chunk 108 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   chunk 110 optimal weight:    9.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.5524

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 521 ASN
F 522 GLN
** C 261 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 = 0.4569 r_free = 0.4569 target = 0.129287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.106384 restraints weight = 40789.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.4145 rms_B_bonded: 5.96
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6882
moved from start:          0.4753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9962  Z= 0.117
  Angle     :  0.613  12.596  13533  Z= 0.311
  Chirality :  0.042   0.218   1500
  Planarity :  0.004   0.062   1744
  Dihedral  :  5.041  43.707   1377
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.59 %
    Favored  : 91.41 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.99 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.06 (0.23), residues: 1222
  helix: -1.13 (0.36), residues: 220
  sheet: -1.51 (0.39), residues: 170
  loop : -2.57 (0.20), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 629 
 TYR   0.035   0.001   TYR C 541 
 PHE   0.025   0.001   PHE H 827 
 TRP   0.008   0.001   TRP F 553 
 HIS   0.002   0.000   HIS C 167 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 9938)
  covalent geometry    : angle       0.61271 /  0.31 (13485)
  SS BOND              : bond        0.00223 /  0.13 (   24)
  SS BOND              : angle       0.72696 /  0.47 (   48)
  hydrogen bonds       : bond        0.03555 /  2.23 (  201)
  hydrogen bonds       : angle       5.88292 /  4.10 (  570)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 118
  time to evaluate  : 0.364 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  352 GLU cc_start: 0.3794 (tp30) cc_final: 0.3568 (mm-30)
REVERT: F  367 GLU cc_start: 0.5026 (OUTLIER) cc_final: 0.3364 (mp0)
REVERT: F  464 ILE cc_start: 0.8189 (mm) cc_final: 0.7726 (tt)
REVERT: F  529 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7825 (tt)
REVERT: F  696 MET cc_start: 0.0943 (mmt) cc_final: 0.0517 (ttm)
REVERT: C   77 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.6301 (t80)
REVERT: C  399 PHE cc_start: 0.5192 (p90) cc_final: 0.4639 (p90)
REVERT: C  479 LEU cc_start: 0.8404 (tt) cc_final: 0.8073 (mp)
REVERT: C  686 MET cc_start: 0.1422 (mtt) cc_final: 0.1081 (mtm)
REVERT: C  913 MET cc_start: 0.7068 (mmt) cc_final: 0.6687 (mmp)
REVERT: C 1056 GLN cc_start: 0.8646 (tp40) cc_final: 0.8409 (tp40)
REVERT: C 1075 LEU cc_start: 0.6560 (pp) cc_final: 0.6310 (pp)
  outliers start: 33
  outliers final: 21
  residues processed: 145
  average time/residue: 0.1061
  time to fit residues: 21.2896
Evaluate side-chains
  124 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  929 VAL
Chi-restraints excluded: chain H residue 1040 LEU
Chi-restraints excluded: chain F residue  367 GLU
Chi-restraints excluded: chain F residue  381 VAL
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  438 TYR
Chi-restraints excluded: chain F residue  460 SER
Chi-restraints excluded: chain F residue  505 ARG
Chi-restraints excluded: chain F residue  512 THR
Chi-restraints excluded: chain F residue  519 ASN
Chi-restraints excluded: chain F residue  529 ILE
Chi-restraints excluded: chain F residue  596 ILE
Chi-restraints excluded: chain F residue  697 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   77 TYR
Chi-restraints excluded: chain C residue  245 ILE
Chi-restraints excluded: chain C residue  274 TYR
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain C residue  470 LYS
Chi-restraints excluded: chain C residue  506 PHE
Chi-restraints excluded: chain C residue  523 TYR
Chi-restraints excluded: chain C residue  564 THR
Chi-restraints excluded: chain C residue  577 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [24, 9, 95, 76, 72, 26, 32, 63, 2, 20, 21]
   chunk 24 optimal weight:   10.0000
   chunk 9 optimal weight:    0.6980
   chunk 95 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 26 optimal weight:    9.9990
   chunk 32 optimal weight:    0.4980
   chunk 63 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 815 GLN
** F 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 GLN
** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 627 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 = 0.4533 r_free = 0.4533 target = 0.126458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.103723 restraints weight = 40892.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.4106 rms_B_bonded: 5.78
r_work (final): 0.4106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.5251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9962  Z= 0.166
  Angle     :  0.636  10.863  13533  Z= 0.329
  Chirality :  0.045   0.259   1500
  Planarity :  0.004   0.064   1744
  Dihedral  :  5.238  43.620   1377
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 16.44 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.96 (0.23), residues: 1222
  helix: -1.15 (0.35), residues: 223
  sheet: -1.43 (0.40), residues: 170
  loop : -2.48 (0.20), residues: 829

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG F 614 
 TYR   0.013   0.001   TYR H 932 
 PHE   0.015   0.001   PHE H 827 
 TRP   0.008   0.001   TRP C 553 
 HIS   0.003   0.001   HIS C 194 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.17 ( 9938)
  covalent geometry    : angle       0.63586 /  0.33 (13485)
  SS BOND              : bond        0.00276 /  0.16 (   24)
  SS BOND              : angle       0.78386 /  0.51 (   48)
  hydrogen bonds       : bond        0.03530 /  2.23 (  201)
  hydrogen bonds       : angle       5.84669 /  4.04 (  570)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 98
  time to evaluate  : 0.385 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  807 LYS cc_start: 0.7960 (pttt) cc_final: 0.7721 (pttp)
REVERT: H  827 PHE cc_start: 0.6156 (m-80) cc_final: 0.5862 (m-80)
REVERT: F  367 GLU cc_start: 0.5414 (OUTLIER) cc_final: 0.3409 (mp0)
REVERT: F  464 ILE cc_start: 0.8142 (mm) cc_final: 0.7881 (mt)
REVERT: F  549 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6712 (mm-30)
REVERT: F  563 MET cc_start: 0.7391 (tpp) cc_final: 0.6764 (mmm)
REVERT: F  696 MET cc_start: 0.1051 (mmt) cc_final: 0.0579 (ttm)
REVERT: C   77 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6035 (t80)
REVERT: C  168 THR cc_start: 0.8409 (m) cc_final: 0.8181 (p)
REVERT: C  240 MET cc_start: 0.5651 (ttt) cc_final: 0.5426 (ttt)
REVERT: C  341 PHE cc_start: 0.8119 (OUTLIER) cc_final: 0.7592 (m-80)
REVERT: C  479 LEU cc_start: 0.8431 (tt) cc_final: 0.8039 (mp)
REVERT: C  686 MET cc_start: 0.1477 (mtt) cc_final: 0.1102 (mtm)
REVERT: C  913 MET cc_start: 0.7128 (mmt) cc_final: 0.6703 (mmp)
REVERT: C 1056 GLN cc_start: 0.8594 (tp40) cc_final: 0.8377 (tp-100)
  outliers start: 39
  outliers final: 32
  residues processed: 131
  average time/residue: 0.1030
  time to fit residues: 18.8461
Evaluate side-chains
  126 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 91
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  929 VAL
Chi-restraints excluded: chain H residue 1040 LEU
Chi-restraints excluded: chain H residue 1061 LEU
Chi-restraints excluded: chain F residue  367 GLU
Chi-restraints excluded: chain F residue  381 VAL
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  438 TYR
Chi-restraints excluded: chain F residue  450 LEU
Chi-restraints excluded: chain F residue  460 SER
Chi-restraints excluded: chain F residue  505 ARG
Chi-restraints excluded: chain F residue  519 ASN
Chi-restraints excluded: chain F residue  529 ILE
Chi-restraints excluded: chain F residue  596 ILE
Chi-restraints excluded: chain F residue  697 LEU
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue   77 TYR
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  245 ILE
Chi-restraints excluded: chain C residue  274 TYR
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain C residue  470 LYS
Chi-restraints excluded: chain C residue  506 PHE
Chi-restraints excluded: chain C residue  523 TYR
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  564 THR
Chi-restraints excluded: chain C residue  567 LEU
Chi-restraints excluded: chain C residue  577 TYR
Chi-restraints excluded: chain C residue  623 VAL
Chi-restraints excluded: chain C residue 1061 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [103, 35, 31, 43, 98, 70, 47, 83, 79, 85, 86]
   chunk 103 optimal weight:    1.9990
   chunk 35 optimal weight:    7.9990
   chunk 31 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   chunk 98 optimal weight:    0.3980
   chunk 70 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 83 optimal weight:    0.4980
   chunk 79 optimal weight:    0.8980
   chunk 85 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 815 GLN
H1072 ASN
F 466 GLN
** F 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 522 GLN
F 602 ASN
** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1084 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.127601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.104886 restraints weight = 40655.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.4127 rms_B_bonded: 5.91
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
moved from start:          0.5431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9962  Z= 0.114
  Angle     :  0.598  13.187  13533  Z= 0.305
  Chirality :  0.044   0.255   1500
  Planarity :  0.004   0.062   1744
  Dihedral  :  5.086  40.981   1377
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 16.53 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.89 (0.23), residues: 1222
  helix: -1.09 (0.36), residues: 210
  sheet: -1.55 (0.39), residues: 180
  loop : -2.38 (0.20), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F 614 
 TYR   0.039   0.001   TYR C 824 
 PHE   0.022   0.001   PHE F 590 
 TRP   0.007   0.001   TRP F 553 
 HIS   0.002   0.000   HIS F 681 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.11 ( 9938)
  covalent geometry    : angle       0.59784 /  0.31 (13485)
  SS BOND              : bond        0.00194 /  0.11 (   24)
  SS BOND              : angle       0.65188 /  0.43 (   48)
  hydrogen bonds       : bond        0.03338 /  2.16 (  201)
  hydrogen bonds       : angle       5.63452 /  3.90 (  570)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 100
  time to evaluate  : 0.296 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  367 GLU cc_start: 0.5123 (OUTLIER) cc_final: 0.3588 (mp0)
REVERT: F  549 GLU cc_start: 0.7649 (mm-30) cc_final: 0.6949 (mm-30)
REVERT: F  563 MET cc_start: 0.7350 (tpp) cc_final: 0.6800 (mmm)
REVERT: F  696 MET cc_start: 0.1116 (mmt) cc_final: 0.0631 (ttm)
REVERT: C   77 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.6059 (t80)
REVERT: C  168 THR cc_start: 0.8481 (m) cc_final: 0.8261 (p)
REVERT: C  341 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7575 (m-80)
REVERT: C  686 MET cc_start: 0.1602 (mtt) cc_final: 0.1189 (mtm)
REVERT: C  830 LYS cc_start: 0.9490 (mtmt) cc_final: 0.9226 (mmtt)
REVERT: C  913 MET cc_start: 0.7191 (mmt) cc_final: 0.6767 (mmp)
  outliers start: 44
  outliers final: 32
  residues processed: 139
  average time/residue: 0.1085
  time to fit residues: 20.8036
Evaluate side-chains
  126 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 91
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  929 VAL
Chi-restraints excluded: chain H residue 1040 LEU
Chi-restraints excluded: chain H residue 1061 LEU
Chi-restraints excluded: chain F residue  367 GLU
Chi-restraints excluded: chain F residue  373 SER
Chi-restraints excluded: chain F residue  381 VAL
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  438 TYR
Chi-restraints excluded: chain F residue  450 LEU
Chi-restraints excluded: chain F residue  460 SER
Chi-restraints excluded: chain F residue  505 ARG
Chi-restraints excluded: chain F residue  519 ASN
Chi-restraints excluded: chain F residue  529 ILE
Chi-restraints excluded: chain F residue  596 ILE
Chi-restraints excluded: chain F residue  635 TYR
Chi-restraints excluded: chain F residue  651 LEU
Chi-restraints excluded: chain F residue  697 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue   77 TYR
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  245 ILE
Chi-restraints excluded: chain C residue  274 TYR
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain C residue  470 LYS
Chi-restraints excluded: chain C residue  506 PHE
Chi-restraints excluded: chain C residue  523 TYR
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  564 THR
Chi-restraints excluded: chain C residue  577 TYR
Chi-restraints excluded: chain C residue  827 PHE
Chi-restraints excluded: chain C residue 1061 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [97, 92, 104, 23, 50, 70, 108, 68, 64, 33, 2]
   chunk 97 optimal weight:    5.9990
   chunk 92 optimal weight:    8.9990
   chunk 104 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0370
   chunk 50 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 108 optimal weight:    8.9990
   chunk 68 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.7664

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 815 GLN
** F 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 602 ASN
** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1031 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.127181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.104484 restraints weight = 40272.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.4119 rms_B_bonded: 5.87
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6923
moved from start:          0.5640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9962  Z= 0.118
  Angle     :  0.616  13.638  13533  Z= 0.312
  Chirality :  0.044   0.332   1500
  Planarity :  0.004   0.060   1744
  Dihedral  :  5.050  41.256   1377
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.17 %
    Favored  : 90.83 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 16.71 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.23), residues: 1222
  helix: -1.07 (0.35), residues: 215
  sheet: -1.61 (0.38), residues: 197
  loop : -2.34 (0.20), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C1057 
 TYR   0.044   0.001   TYR H 824 
 PHE   0.017   0.001   PHE H 827 
 TRP   0.007   0.001   TRP F 553 
 HIS   0.002   0.000   HIS C 194 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00265 /  0.12 ( 9938)
  covalent geometry    : angle       0.61588 /  0.31 (13485)
  SS BOND              : bond        0.00195 /  0.12 (   24)
  SS BOND              : angle       0.68328 /  0.45 (   48)
  hydrogen bonds       : bond        0.03286 /  2.14 (  201)
  hydrogen bonds       : angle       5.47435 /  3.78 (  570)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 99
  time to evaluate  : 0.281 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  367 GLU cc_start: 0.5110 (OUTLIER) cc_final: 0.2135 (mt-10)
REVERT: F  433 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7906 (pt)
REVERT: F  464 ILE cc_start: 0.8371 (mm) cc_final: 0.8138 (mp)
REVERT: F  549 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6931 (mm-30)
REVERT: F  563 MET cc_start: 0.7294 (tpp) cc_final: 0.6824 (mmm)
REVERT: F  696 MET cc_start: 0.1194 (mmt) cc_final: 0.0685 (ttm)
REVERT: C   77 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.6089 (t80)
REVERT: C  341 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7522 (m-80)
REVERT: C  686 MET cc_start: 0.1769 (mtt) cc_final: 0.1245 (mtm)
REVERT: C  830 LYS cc_start: 0.9509 (mtmt) cc_final: 0.9244 (mmtt)
REVERT: C  913 MET cc_start: 0.7179 (mmt) cc_final: 0.6738 (mmp)
  outliers start: 43
  outliers final: 34
  residues processed: 136
  average time/residue: 0.1062
  time to fit residues: 19.6718
Evaluate side-chains
  133 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 95
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  820 LEU
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  929 VAL
Chi-restraints excluded: chain H residue 1040 LEU
Chi-restraints excluded: chain H residue 1061 LEU
Chi-restraints excluded: chain F residue  367 GLU
Chi-restraints excluded: chain F residue  373 SER
Chi-restraints excluded: chain F residue  381 VAL
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  433 ILE
Chi-restraints excluded: chain F residue  438 TYR
Chi-restraints excluded: chain F residue  450 LEU
Chi-restraints excluded: chain F residue  460 SER
Chi-restraints excluded: chain F residue  505 ARG
Chi-restraints excluded: chain F residue  529 ILE
Chi-restraints excluded: chain F residue  596 ILE
Chi-restraints excluded: chain F residue  635 TYR
Chi-restraints excluded: chain F residue  697 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue   77 TYR
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  245 ILE
Chi-restraints excluded: chain C residue  274 TYR
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain C residue  470 LYS
Chi-restraints excluded: chain C residue  506 PHE
Chi-restraints excluded: chain C residue  523 TYR
Chi-restraints excluded: chain C residue  532 SER
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  564 THR
Chi-restraints excluded: chain C residue  567 LEU
Chi-restraints excluded: chain C residue  577 TYR
Chi-restraints excluded: chain C residue 1061 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [28, 39, 1, 30, 53, 72, 15, 75, 55, 64, 3]
   chunk 28 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0770
   chunk 53 optimal weight:    4.9990
   chunk 72 optimal weight:    0.0370
   chunk 15 optimal weight:   10.0000
   chunk 75 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.7418

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.127226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.105966 restraints weight = 40606.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.4134 rms_B_bonded: 5.09
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6877
moved from start:          0.5809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9962  Z= 0.115
  Angle     :  0.614  14.679  13533  Z= 0.309
  Chirality :  0.044   0.280   1500
  Planarity :  0.004   0.061   1744
  Dihedral  :  5.031  40.758   1377
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.41 %
    Favored  : 90.59 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 17.26 %
    Favored  : 78.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.79 (0.23), residues: 1222
  helix: -1.05 (0.35), residues: 216
  sheet: -1.54 (0.38), residues: 195
  loop : -2.30 (0.20), residues: 811

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 505 
 TYR   0.024   0.001   TYR H 824 
 PHE   0.015   0.001   PHE F 590 
 TRP   0.009   0.001   TRP F 553 
 HIS   0.002   0.000   HIS C 194 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 9938)
  covalent geometry    : angle       0.61384 /  0.31 (13485)
  SS BOND              : bond        0.00188 /  0.11 (   24)
  SS BOND              : angle       0.72960 /  0.48 (   48)
  hydrogen bonds       : bond        0.03233 /  2.10 (  201)
  hydrogen bonds       : angle       5.42101 /  3.73 (  570)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 95
  time to evaluate  : 0.382 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  367 GLU cc_start: 0.5171 (OUTLIER) cc_final: 0.2141 (mt-10)
REVERT: F  433 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7971 (pt)
REVERT: F  464 ILE cc_start: 0.8377 (mm) cc_final: 0.8114 (mt)
REVERT: F  549 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7009 (mm-30)
REVERT: F  563 MET cc_start: 0.7425 (tpp) cc_final: 0.6927 (mmm)
REVERT: F  614 ARG cc_start: 0.8232 (tpp80) cc_final: 0.7905 (mmm-85)
REVERT: F  696 MET cc_start: 0.1043 (mmt) cc_final: 0.0507 (ttm)
REVERT: C   77 TYR cc_start: 0.7372 (OUTLIER) cc_final: 0.6072 (t80)
REVERT: C  341 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7529 (m-80)
REVERT: C  686 MET cc_start: 0.1770 (mtt) cc_final: 0.1327 (mtm)
REVERT: C  830 LYS cc_start: 0.9528 (mtmt) cc_final: 0.9280 (mmtt)
REVERT: C  913 MET cc_start: 0.7122 (mmt) cc_final: 0.6703 (mmp)
REVERT: C 1075 LEU cc_start: 0.6666 (pp) cc_final: 0.6416 (pp)
  outliers start: 41
  outliers final: 32
  residues processed: 130
  average time/residue: 0.1065
  time to fit residues: 19.0028
Evaluate side-chains
  130 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 94
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  820 LEU
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  929 VAL
Chi-restraints excluded: chain H residue 1040 LEU
Chi-restraints excluded: chain H residue 1053 ASP
Chi-restraints excluded: chain H residue 1061 LEU
Chi-restraints excluded: chain F residue  367 GLU
Chi-restraints excluded: chain F residue  373 SER
Chi-restraints excluded: chain F residue  381 VAL
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  433 ILE
Chi-restraints excluded: chain F residue  438 TYR
Chi-restraints excluded: chain F residue  450 LEU
Chi-restraints excluded: chain F residue  460 SER
Chi-restraints excluded: chain F residue  505 ARG
Chi-restraints excluded: chain F residue  529 ILE
Chi-restraints excluded: chain F residue  596 ILE
Chi-restraints excluded: chain F residue  635 TYR
Chi-restraints excluded: chain F residue  697 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue   77 TYR
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  245 ILE
Chi-restraints excluded: chain C residue  274 TYR
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain C residue  470 LYS
Chi-restraints excluded: chain C residue  506 PHE
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  564 THR
Chi-restraints excluded: chain C residue  577 TYR
Chi-restraints excluded: chain C residue 1061 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [13, 15, 31, 113, 83, 110, 104, 108, 89, 38, 94]
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    9.9990
   chunk 31 optimal weight:    9.9990
   chunk 113 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 110 optimal weight:    3.9990
   chunk 104 optimal weight:    6.9990
   chunk 108 optimal weight:    0.0870
   chunk 89 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 94 optimal weight:    0.3980
   overall best weight:    1.0760

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.125886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.103099 restraints weight = 39987.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.4101 rms_B_bonded: 5.68
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.6041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9962  Z= 0.133
  Angle     :  0.623  13.752  13533  Z= 0.315
  Chirality :  0.044   0.273   1500
  Planarity :  0.004   0.060   1744
  Dihedral  :  5.066  41.175   1375
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.82 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 16.99 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.76 (0.23), residues: 1222
  helix: -0.80 (0.36), residues: 210
  sheet: -1.67 (0.36), residues: 217
  loop : -2.30 (0.21), residues: 795

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F 629 
 TYR   0.016   0.001   TYR H 824 
 PHE   0.012   0.001   PHE H 814 
 TRP   0.007   0.001   TRP F 553 
 HIS   0.004   0.001   HIS F 681 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.13 ( 9938)
  covalent geometry    : angle       0.62318 /  0.32 (13485)
  SS BOND              : bond        0.00225 /  0.13 (   24)
  SS BOND              : angle       0.67341 /  0.44 (   48)
  hydrogen bonds       : bond        0.03195 /  2.06 (  201)
  hydrogen bonds       : angle       5.57758 /  3.82 (  570)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 97
  time to evaluate  : 0.290 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  917 PRO cc_start: 0.5330 (Cg_endo) cc_final: 0.5002 (Cg_exo)
REVERT: F  367 GLU cc_start: 0.5461 (OUTLIER) cc_final: 0.3502 (mp0)
REVERT: F  433 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8030 (pt)
REVERT: F  464 ILE cc_start: 0.8359 (mm) cc_final: 0.7924 (tt)
REVERT: F  529 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8029 (tt)
REVERT: F  549 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7171 (mm-30)
REVERT: F  563 MET cc_start: 0.7500 (tpp) cc_final: 0.7108 (mmm)
REVERT: F  696 MET cc_start: 0.1420 (mmt) cc_final: 0.0824 (ttm)
REVERT: C   77 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.5954 (t80)
REVERT: C  278 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7341 (mtm)
REVERT: C  341 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7521 (m-80)
REVERT: C  686 MET cc_start: 0.1840 (mtt) cc_final: 0.1300 (mtm)
REVERT: C  830 LYS cc_start: 0.9564 (mtmt) cc_final: 0.9336 (mmtt)
REVERT: C  913 MET cc_start: 0.7284 (mmt) cc_final: 0.6992 (mmm)
REVERT: C 1075 LEU cc_start: 0.6755 (pp) cc_final: 0.6521 (pp)
  outliers start: 41
  outliers final: 34
  residues processed: 131
  average time/residue: 0.1152
  time to fit residues: 20.6669
Evaluate side-chains
  131 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 91
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  820 LEU
Chi-restraints excluded: chain H residue  821 LEU
Chi-restraints excluded: chain H residue  929 VAL
Chi-restraints excluded: chain H residue 1040 LEU
Chi-restraints excluded: chain H residue 1053 ASP
Chi-restraints excluded: chain H residue 1061 LEU
Chi-restraints excluded: chain F residue  367 GLU
Chi-restraints excluded: chain F residue  373 SER
Chi-restraints excluded: chain F residue  381 VAL
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  433 ILE
Chi-restraints excluded: chain F residue  438 TYR
Chi-restraints excluded: chain F residue  450 LEU
Chi-restraints excluded: chain F residue  460 SER
Chi-restraints excluded: chain F residue  480 ILE
Chi-restraints excluded: chain F residue  505 ARG
Chi-restraints excluded: chain F residue  529 ILE
Chi-restraints excluded: chain F residue  587 LYS
Chi-restraints excluded: chain F residue  596 ILE
Chi-restraints excluded: chain F residue  635 TYR
Chi-restraints excluded: chain F residue  697 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue   77 TYR
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  245 ILE
Chi-restraints excluded: chain C residue  274 TYR
Chi-restraints excluded: chain C residue  278 MET
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  344 LEU
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain C residue  470 LYS
Chi-restraints excluded: chain C residue  506 PHE
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  555 VAL
Chi-restraints excluded: chain C residue  564 THR
Chi-restraints excluded: chain C residue  577 TYR
Chi-restraints excluded: chain C residue 1061 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [64, 14, 26, 29, 54, 22, 94, 20, 53, 96, 111]
   chunk 64 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0370
   chunk 26 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 96 optimal weight:    7.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    1.8064

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 264 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 516 GLN
C 568 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.122673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.099505 restraints weight = 40217.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.4046 rms_B_bonded: 5.83
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7072
moved from start:          0.6646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9962  Z= 0.196
  Angle     :  0.705  14.458  13533  Z= 0.362
  Chirality :  0.046   0.326   1500
  Planarity :  0.005   0.059   1744
  Dihedral  :  5.482  43.517   1375
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 17.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.05 %
    Favored  : 88.95 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 17.72 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.23), residues: 1222
  helix: -0.84 (0.35), residues: 222
  sheet: -1.27 (0.39), residues: 188
  loop : -2.48 (0.20), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F 694 
 TYR   0.039   0.002   TYR C 540 
 PHE   0.019   0.002   PHE F 590 
 TRP   0.012   0.002   TRP F 553 
 HIS   0.008   0.001   HIS F 681 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00432 /  0.20 ( 9938)
  covalent geometry    : angle       0.70474 /  0.36 (13485)
  SS BOND              : bond        0.00317 /  0.20 (   24)
  SS BOND              : angle       0.84695 /  0.54 (   48)
  hydrogen bonds       : bond        0.03596 /  2.31 (  201)
  hydrogen bonds       : angle       5.89837 /  4.00 (  570)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 97
  time to evaluate  : 0.391 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H  809 TYR cc_start: 0.7159 (t80) cc_final: 0.6939 (t80)
REVERT: H  917 PRO cc_start: 0.5114 (Cg_endo) cc_final: 0.4829 (Cg_exo)
REVERT: F  367 GLU cc_start: 0.5920 (OUTLIER) cc_final: 0.3263 (mp0)
REVERT: F  417 LEU cc_start: 0.8321 (pt) cc_final: 0.8044 (pt)
REVERT: F  433 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8174 (pt)
REVERT: F  464 ILE cc_start: 0.8292 (mm) cc_final: 0.7906 (tt)
REVERT: F  549 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7227 (mm-30)
REVERT: F  696 MET cc_start: 0.1718 (mmt) cc_final: 0.1118 (ttm)
REVERT: C   77 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.6012 (t80)
REVERT: C  278 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7220 (mtm)
REVERT: C  341 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7457 (m-80)
REVERT: C  563 MET cc_start: 0.3773 (mmm) cc_final: 0.3440 (tpt)
REVERT: C  686 MET cc_start: 0.1956 (mtt) cc_final: 0.1247 (mtm)
REVERT: C  830 LYS cc_start: 0.9594 (mtmt) cc_final: 0.9378 (mmtt)
REVERT: C 1075 LEU cc_start: 0.6674 (pp) cc_final: 0.6428 (pp)
  outliers start: 39
  outliers final: 32
  residues processed: 129
  average time/residue: 0.1050
  time to fit residues: 18.8262
Evaluate side-chains
  128 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 91
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  820 LEU
Chi-restraints excluded: chain H residue  929 VAL
Chi-restraints excluded: chain H residue 1040 LEU
Chi-restraints excluded: chain H residue 1053 ASP
Chi-restraints excluded: chain H residue 1061 LEU
Chi-restraints excluded: chain F residue  367 GLU
Chi-restraints excluded: chain F residue  373 SER
Chi-restraints excluded: chain F residue  381 VAL
Chi-restraints excluded: chain F residue  412 THR
Chi-restraints excluded: chain F residue  433 ILE
Chi-restraints excluded: chain F residue  438 TYR
Chi-restraints excluded: chain F residue  450 LEU
Chi-restraints excluded: chain F residue  460 SER
Chi-restraints excluded: chain F residue  480 ILE
Chi-restraints excluded: chain F residue  505 ARG
Chi-restraints excluded: chain F residue  529 ILE
Chi-restraints excluded: chain F residue  587 LYS
Chi-restraints excluded: chain F residue  596 ILE
Chi-restraints excluded: chain F residue  635 TYR
Chi-restraints excluded: chain F residue  697 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   63 THR
Chi-restraints excluded: chain C residue   77 TYR
Chi-restraints excluded: chain C residue   96 THR
Chi-restraints excluded: chain C residue  102 VAL
Chi-restraints excluded: chain C residue  245 ILE
Chi-restraints excluded: chain C residue  274 TYR
Chi-restraints excluded: chain C residue  278 MET
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  383 CYS
Chi-restraints excluded: chain C residue  470 LYS
Chi-restraints excluded: chain C residue  506 PHE
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  555 VAL
Chi-restraints excluded: chain C residue  577 TYR
Chi-restraints excluded: chain C residue 1061 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks: [55, 25, 16, 102, 68, 26, 1, 71, 40, 52, 91]
   chunk 55 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 102 optimal weight:    0.0060
   chunk 68 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.6996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  60 GLN
** C 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.124933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.102025 restraints weight = 40627.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.4086 rms_B_bonded: 5.85
r_work (final): 0.4086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
moved from start:          0.6591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   9962  Z= 0.118
  Angle     :  0.643  14.759  13533  Z= 0.323
  Chirality :  0.044   0.288   1500
  Planarity :  0.004   0.060   1744
  Dihedral  :  5.093  40.917   1374
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.08 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.63 %
    Favored  : 78.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.23), residues: 1222
  helix: -0.61 (0.37), residues: 198
  sheet: -1.47 (0.39), residues: 191
  loop : -2.29 (0.20), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F 614 
 TYR   0.014   0.001   TYR H 824 
 PHE   0.010   0.001   PHE C 101 
 TRP   0.007   0.001   TRP F 553 
 HIS   0.006   0.001   HIS F 681 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 9938)
  covalent geometry    : angle       0.64322 /  0.32 (13485)
  SS BOND              : bond        0.00203 /  0.12 (   24)
  SS BOND              : angle       0.68486 /  0.46 (   48)
  hydrogen bonds       : bond        0.03238 /  2.09 (  201)
  hydrogen bonds       : angle       5.54642 /  3.78 (  570)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2622.47 seconds
wall clock time: 45 minutes 44.85 seconds (2744.85 seconds total)