Starting phenix.real_space_refine
on Tue Mar  3 17:59:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yaj_33714/03_2026/7yaj_33714.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yaj_33714/03_2026/7yaj_33714.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yaj_33714/03_2026/7yaj_33714.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yaj_33714/03_2026/7yaj_33714.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yaj_33714/03_2026/7yaj_33714.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yaj_33714/03_2026/7yaj_33714.map"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Mn      1      7.51       5
     P       3      5.49       5
     S      55      5.16       5
     C    4860      2.51       5
     N    1283      2.21       5
     O    1447      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7649
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 874, 6675
          Classifications: {'peptide': 874}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 34, 'TRANS': 839}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "C"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 942
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MN': 1, 'ACP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.72, per 1000 atoms: 0.22
  Number of scatterers: 7649
  At special positions: 0
  Unit cell: (75.845, 82.74, 134.945, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      1     24.99
     S      55     16.00
     P       3     15.00
     O    1447      8.00
     N    1283      7.00
     C    4860      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  55 " - pdb=" SG  CYS C 128 " 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: 0.63
  Conformation dependent library (CDL) restraints added in 261.4 milliseconds
  

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1842

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 9 sheets defined
      50.5% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 29
    Processing helix  chain 'A' and resid 30 through 38
    Processing helix  chain 'A' and resid 47 through 59
      removed outlier: 3.800A  pdb=" N   PHE A  57 " --> pdb=" O   HIS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 78
      removed outlier: 3.864A  pdb=" N   GLN A  78 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 97
    Processing helix  chain 'A' and resid 99 through 135
      removed outlier: 3.630A  pdb=" N   ALA A 103 " --> pdb=" O   GLN A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 240
      removed outlier: 3.972A  pdb=" N   ASN A 238 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   SER A 239 " --> pdb=" O   GLY A 236 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   GLU A 240 " --> pdb=" O   GLU A 237 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 235 through 240'
    Processing helix  chain 'A' and resid 241 through 249
      removed outlier: 3.922A  pdb=" N   PHE A 245 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 288
    Processing helix  chain 'A' and resid 290 through 306
    Processing helix  chain 'A' and resid 309 through 328
    Processing helix  chain 'A' and resid 335 through 341
      removed outlier: 4.007A  pdb=" N   GLU A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 407
    Processing helix  chain 'A' and resid 424 through 438
    Processing helix  chain 'A' and resid 441 through 446
    Processing helix  chain 'A' and resid 482 through 490
    Processing helix  chain 'A' and resid 503 through 521
    Processing helix  chain 'A' and resid 551 through 561
      removed outlier: 3.761A  pdb=" N   ALA A 555 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 584
    Processing helix  chain 'A' and resid 595 through 602
    Processing helix  chain 'A' and resid 603 through 611
    Processing helix  chain 'A' and resid 621 through 635
      removed outlier: 3.800A  pdb=" N   ASN A 635 " --> pdb=" O   SER A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 649 through 655
    Processing helix  chain 'A' and resid 666 through 673
    Processing helix  chain 'A' and resid 682 through 724
      removed outlier: 3.760A  pdb=" N   MET A 686 " --> pdb=" O   PHE A 682 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   TYR A 696 " --> pdb=" O   GLY A 692 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ASN A 697 " --> pdb=" O   LYS A 693 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 743
    Processing helix  chain 'A' and resid 743 through 750
      removed outlier: 3.975A  pdb=" N   LEU A 749 " --> pdb=" O   PRO A 745 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 755 through 760
    Processing helix  chain 'A' and resid 772 through 798
    Processing helix  chain 'A' and resid 804 through 826
      removed outlier: 3.988A  pdb=" N   THR A 808 " --> pdb=" O   THR A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 837
      removed outlier: 3.663A  pdb=" N   ILE A 836 " --> pdb=" O   SER A 832 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLY A 837 " --> pdb=" O   VAL A 833 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 832 through 837'
    Processing helix  chain 'A' and resid 841 through 861
      removed outlier: 3.505A  pdb=" N   CYS A 845 " --> pdb=" O   ASN A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 868
    Processing helix  chain 'A' and resid 874 through 904
      removed outlier: 4.546A  pdb=" N   VAL A 888 " --> pdb=" O   LEU A 884 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   CYS A 889 " --> pdb=" O   THR A 885 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 123
    Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 151
      removed outlier: 4.222A  pdb=" N   HIS A 140 " --> pdb=" O   CYS A 162 " (cutoff:3.500A)
      removed outlier: 4.934A  pdb=" N   THR A 160 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ALA A 228 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   VAL A 223 " --> pdb=" O   SER A 182 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   SER A 182 " --> pdb=" O   VAL A 223 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   CYS A 225 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ASP A 180 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.027A  pdb=" N   LYS A 227 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 5.721A  pdb=" N   ALA A 178 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   LYS A 229 " --> pdb=" O   PHE A 176 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   ASP A 172 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 332
      removed outlier: 6.066A  pdb=" N   GLY A 658 " --> pdb=" O   MET A 675 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   LEU A 677 " --> pdb=" O   GLY A 658 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ALA A 660 " --> pdb=" O   LEU A 677 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   VAL A 639 " --> pdb=" O   ILE A 657 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   VAL A 659 " --> pdb=" O   VAL A 639 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   MET A 641 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
      removed outlier: 8.079A  pdb=" N   MET A 661 " --> pdb=" O   MET A 641 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   VAL A 638 " --> pdb=" O   CYS A 344 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 391 through 392
      removed outlier: 3.522A  pdb=" N   GLU A 374 " --> pdb=" O   ILE A 387 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   THR A 363 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   GLY A 543 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   ILE A 365 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   LEU A 541 " --> pdb=" O   ILE A 365 " (cutoff:3.500A)
      removed outlier: 4.989A  pdb=" N   THR A 367 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   LEU A 539 " --> pdb=" O   THR A 367 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   PHE A 538 " --> pdb=" O   SER A 529 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   SER A 529 " --> pdb=" O   PHE A 538 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLY A 540 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LEU A 525 " --> pdb=" O   VAL A 542 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LYS A 464 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ALA A 450 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   VAL A 466 " --> pdb=" O   ARG A 448 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   ARG A 448 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 392
      removed outlier: 3.522A  pdb=" N   GLU A 374 " --> pdb=" O   ILE A 387 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   THR A 363 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   GLY A 543 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   ILE A 365 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   LEU A 541 " --> pdb=" O   ILE A 365 " (cutoff:3.500A)
      removed outlier: 4.989A  pdb=" N   THR A 367 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   LEU A 539 " --> pdb=" O   THR A 367 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   THR A 492 " --> pdb=" O   PHE A 538 " (cutoff:3.500A)
      removed outlier: 8.301A  pdb=" N   GLY A 540 " --> pdb=" O   THR A 492 " (cutoff:3.500A)
      removed outlier: 9.873A  pdb=" N   GLN A 494 " --> pdb=" O   GLY A 540 " (cutoff:3.500A)
      removed outlier: 13.486A  pdb=" N   VAL A 542 " --> pdb=" O   GLN A 494 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 416 through 417
    Processing sheet with id=AA6, first strand: chain 'A' and resid 592 through 594
      removed outlier: 8.212A  pdb=" N   GLN A 592 " --> pdb=" O   ALA A 615 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   PHE A 617 " --> pdb=" O   GLN A 592 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   VAL A 594 " --> pdb=" O   PHE A 617 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 40
      removed outlier: 3.825A  pdb=" N   LEU C  51 " --> pdb=" O   MET C 115 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   MET C 115 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   SER C 103 " --> pdb=" O   TYR C 112 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 92
      removed outlier: 4.831A  pdb=" N   PHE C  80 " --> pdb=" O   ARG C  71 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   ARG C  71 " --> pdb=" O   PHE C  80 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C 131 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL C 130 " --> pdb=" O   TYR C 148 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   TYR C 148 " --> pdb=" O   VAL C 130 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 90 through 92
      removed outlier: 4.831A  pdb=" N   PHE C  80 " --> pdb=" O   ARG C  71 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   ARG C  71 " --> pdb=" O   PHE C  80 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C 131 " (cutoff:3.500A)

    445 hydrogen bonds defined for protein.
    1293 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: 1.41

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1466
        1.33 -     1.45: 1767
        1.45 -     1.58: 4450
        1.58 -     1.70: 3
        1.70 -     1.82: 90
  Bond restraints: 7776
  Sorted by residual:
  bond pdb=" O3A ACP A1001 "
       pdb=" PB  ACP A1001 "
    ideal  model  delta    sigma   weight residual
    1.698  1.608  0.090 2.00e-02 2.50e+03 2.02e+01
  bond pdb=" C3B ACP A1001 "
       pdb=" PG  ACP A1001 "
    ideal  model  delta    sigma   weight residual
    1.875  1.795  0.080 2.00e-02 2.50e+03 1.61e+01
  bond pdb=" O5' ACP A1001 "
       pdb=" PA  ACP A1001 "
    ideal  model  delta    sigma   weight residual
    1.659  1.580  0.079 2.00e-02 2.50e+03 1.56e+01
  bond pdb=" N   ILE A 431 "
       pdb=" CA  ILE A 431 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.17e-02 7.31e+03 1.00e+01
  bond pdb=" N   VAL A 415 "
       pdb=" CA  VAL A 415 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.035 1.14e-02 7.69e+03 9.64e+00
  ... (remaining 7771 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.79: 10308
        2.79 -     5.58: 190
        5.58 -     8.37: 23
        8.37 -    11.16: 7
       11.16 -    13.94: 4
  Bond angle restraints: 10532
  Sorted by residual:
  angle pdb=" PA  ACP A1001 "
        pdb=" O3A ACP A1001 "
        pdb=" PB  ACP A1001 "
      ideal   model   delta    sigma   weight residual
     125.06  111.12   13.94 3.00e+00 1.11e-01 2.16e+01
  angle pdb=" N   ALA A 407 "
        pdb=" CA  ALA A 407 "
        pdb=" C   ALA A 407 "
      ideal   model   delta    sigma   weight residual
     113.19  108.48    4.71 1.19e+00 7.06e-01 1.57e+01
  angle pdb=" CB  MET A  97 "
        pdb=" CG  MET A  97 "
        pdb=" SD  MET A  97 "
      ideal   model   delta    sigma   weight residual
     112.70  124.31  -11.61 3.00e+00 1.11e-01 1.50e+01
  angle pdb=" N   GLN A 443 "
        pdb=" CA  GLN A 443 "
        pdb=" C   GLN A 443 "
      ideal   model   delta    sigma   weight residual
     111.28  107.08    4.20 1.09e+00 8.42e-01 1.48e+01
  angle pdb=" N   LEU A 442 "
        pdb=" CA  LEU A 442 "
        pdb=" C   LEU A 442 "
      ideal   model   delta    sigma   weight residual
     112.54  107.99    4.55 1.22e+00 6.72e-01 1.39e+01
  ... (remaining 10527 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.80: 4221
       24.80 -    49.60: 437
       49.60 -    74.40: 56
       74.40 -    99.20: 7
       99.20 -   124.00: 2
  Dihedral angle restraints: 4723
    sinusoidal: 1863
      harmonic: 2860
  Sorted by residual:
  dihedral pdb=" CB  CYS C  55 "
           pdb=" SG  CYS C  55 "
           pdb=" SG  CYS C 128 "
           pdb=" CB  CYS C 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.99  -73.99     1      1.00e+01 1.00e-02 6.95e+01
  dihedral pdb=" CA  HIS A  98 "
           pdb=" C   HIS A  98 "
           pdb=" N   GLN A  99 "
           pdb=" CA  GLN A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.81   24.19     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" O1A ACP A1001 "
           pdb=" O3A ACP A1001 "
           pdb=" PA  ACP A1001 "
           pdb=" PB  ACP A1001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -48.75   75.25 -124.00     1      3.00e+01 1.11e-03 1.66e+01
  ... (remaining 4720 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 987
       0.061 -    0.122: 209
       0.122 -    0.184: 36
       0.184 -    0.245: 10
       0.245 -    0.306: 1
  Chirality restraints: 1243
  Sorted by residual:
  chirality pdb=" CB  ILE A 699 "
            pdb=" CA  ILE A 699 "
            pdb=" CG1 ILE A 699 "
            pdb=" CG2 ILE A 699 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.34e+00
  chirality pdb=" CB  VAL A 611 "
            pdb=" CA  VAL A 611 "
            pdb=" CG1 VAL A 611 "
            pdb=" CG2 VAL A 611 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  ILE A 685 "
            pdb=" N   ILE A 685 "
            pdb=" C   ILE A 685 "
            pdb=" CB  ILE A 685 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1240 not shown)

  Planarity restraints: 1327
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 448 "    0.332 9.50e-02 1.11e+02   1.49e-01 1.35e+01
        pdb=" NE  ARG A 448 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 448 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 448 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 448 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 583 "   -0.317 9.50e-02 1.11e+02   1.42e-01 1.24e+01
        pdb=" NE  ARG A 583 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 583 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 583 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 583 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 744 "   -0.054 5.00e-02 4.00e+02   7.99e-02 1.02e+01
        pdb=" N   PRO A 745 "    0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO A 745 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 745 "   -0.045 5.00e-02 4.00e+02
  ... (remaining 1324 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 234
        2.70 -     3.25: 7495
        3.25 -     3.80: 13133
        3.80 -     4.35: 16135
        4.35 -     4.90: 26696
  Nonbonded interactions: 63693
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 742 "
            pdb="MN    MN A1002 "
     model   vdw
     2.150 2.320
  nonbonded pdb=" O   VAL A 303 "
            pdb="MN    MN A1002 "
     model   vdw
     2.275 2.320
  nonbonded pdb=" OE1 GLU A 513 "
            pdb=" OH  TYR C 143 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OG  SER A 456 "
            pdb=" O2A ACP A1001 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   SER C 145 "
            pdb=" OG  SER C 145 "
     model   vdw
     2.279 3.040
  ... (remaining 63688 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:             1.310
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.180
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6647
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      :  0.005   0.090   7777  Z= 0.306
  Angle     :  0.947  13.944  10534  Z= 0.542
  Chirality :  0.054   0.306   1243
  Planarity :  0.009   0.149   1327
  Dihedral  : 18.800 124.004   2878
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 30.37 %
    Favored  : 67.97 %
  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: -1.00 (0.24), residues: 987
  helix: -0.23 (0.22), residues: 477
  sheet: -0.85 (0.50), residues: 107
  loop : -0.98 (0.28), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  99 
 TYR   0.027   0.003   TYR C 143 
 PHE   0.020   0.002   PHE A 383 
 TRP   0.042   0.002   TRP C 149 
 HIS   0.008   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 7776)
  covalent geometry    : angle       0.94713 (10532)
  SS BOND              : bond        0.00000 (    1)
  SS BOND              : angle       1.44202 (    2)
  hydrogen bonds       : bond        0.18399 (  423)
  hydrogen bonds       : angle       7.43052 ( 1293)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 187
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 ASP cc_start: 0.3003 (m-30) cc_final: 0.2693 (m-30)
REVERT: A  725 PHE cc_start: 0.5297 (OUTLIER) cc_final: 0.4786 (t80)
  outliers start: 14
  outliers final: 4
  residues processed: 195
  average time/residue: 0.0936
  time to fit residues: 24.1584
Evaluate side-chains
  140 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 135
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  725 PHE
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  884 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    0.0570
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.7702

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

Flipped N/Q/H residues before XYZ refinement:
A  53 HIS
** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 727 ASN
A 841 ASN
** C  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.125379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.098749 restraints weight = 22270.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 4.38
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7777  Z= 0.144
  Angle     :  0.665   7.697  10534  Z= 0.344
  Chirality :  0.043   0.154   1243
  Planarity :  0.005   0.067   1327
  Dihedral  :  9.457 120.636   1096
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 30.37 %
    Favored  : 65.72 %
  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: -0.25 (0.25), residues: 987
  helix:  0.55 (0.22), residues: 481
  sheet: -0.87 (0.44), residues: 130
  loop : -0.70 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 417 
 TYR   0.023   0.002   TYR C 143 
 PHE   0.027   0.002   PHE C 100 
 TRP   0.025   0.002   TRP A 766 
 HIS   0.008   0.002   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7776)
  covalent geometry    : angle       0.66443 (10532)
  SS BOND              : bond        0.00195 (    1)
  SS BOND              : angle       1.11525 (    2)
  hydrogen bonds       : bond        0.04551 (  423)
  hydrogen bonds       : angle       5.14492 ( 1293)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 149
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 ASP cc_start: 0.3321 (m-30) cc_final: 0.2881 (m-30)
REVERT: A  131 LEU cc_start: 0.7889 (tp) cc_final: 0.7683 (tp)
REVERT: A  167 ASP cc_start: 0.5080 (OUTLIER) cc_final: 0.4821 (m-30)
REVERT: A  320 LEU cc_start: 0.8424 (tt) cc_final: 0.8037 (pp)
REVERT: A  339 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7749 (pt0)
REVERT: A  412 ASN cc_start: 0.7058 (m-40) cc_final: 0.6550 (m110)
REVERT: A  458 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7259 (tt0)
REVERT: A  459 LYS cc_start: 0.7889 (mtmm) cc_final: 0.7356 (ttmm)
REVERT: A  853 MET cc_start: 0.7459 (tmm) cc_final: 0.7241 (tmm)
REVERT: C   51 LEU cc_start: 0.7635 (tt) cc_final: 0.7157 (mp)
REVERT: C   99 ARG cc_start: 0.7836 (ptt-90) cc_final: 0.6466 (ptt-90)
  outliers start: 33
  outliers final: 16
  residues processed: 175
  average time/residue: 0.0849
  time to fit residues: 19.9564
Evaluate side-chains
  147 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  406 GLU
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  458 GLN
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  668 VAL
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  894 ILE
Chi-restraints excluded: chain C residue   72 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 80 optimal weight:    9.9990
   chunk 90 optimal weight:   10.0000
   chunk 68 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 47 optimal weight:    8.9990
   chunk 72 optimal weight:    7.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
A 140 HIS
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 506 GLN
** C  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.121683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.095176 restraints weight = 22482.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 4.36
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.3120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7777  Z= 0.170
  Angle     :  0.664  13.108  10534  Z= 0.341
  Chirality :  0.043   0.143   1243
  Planarity :  0.005   0.059   1327
  Dihedral  :  9.080 124.794   1090
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 30.13 %
    Favored  : 64.06 %
  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:  0.00 (0.26), residues: 987
  helix:  0.75 (0.22), residues: 489
  sheet: -0.84 (0.44), residues: 133
  loop : -0.53 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  78 
 TYR   0.020   0.002   TYR C 127 
 PHE   0.024   0.002   PHE A 218 
 TRP   0.028   0.002   TRP A 766 
 HIS   0.005   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 7776)
  covalent geometry    : angle       0.66352 (10532)
  SS BOND              : bond        0.00386 (    1)
  SS BOND              : angle       1.53296 (    2)
  hydrogen bonds       : bond        0.04238 (  423)
  hydrogen bonds       : angle       4.94920 ( 1293)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 138
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.3217 (OUTLIER) cc_final: 0.3001 (tt0)
REVERT: A   85 MET cc_start: 0.7445 (mpp) cc_final: 0.7172 (mpp)
REVERT: A  101 ASP cc_start: 0.2899 (m-30) cc_final: 0.2659 (m-30)
REVERT: A  167 ASP cc_start: 0.5456 (OUTLIER) cc_final: 0.5136 (m-30)
REVERT: A  320 LEU cc_start: 0.8413 (tt) cc_final: 0.8081 (pp)
REVERT: A  323 MET cc_start: 0.7450 (mmm) cc_final: 0.6996 (tpp)
REVERT: A  339 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8023 (pt0)
REVERT: A  412 ASN cc_start: 0.7160 (m-40) cc_final: 0.6712 (m110)
REVERT: A  437 MET cc_start: 0.8336 (tpt) cc_final: 0.7993 (tpt)
REVERT: A  458 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7427 (tt0)
REVERT: A  803 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6405 (tp)
REVERT: A  871 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7534 (pm20)
REVERT: C   51 LEU cc_start: 0.7816 (tt) cc_final: 0.7089 (mp)
  outliers start: 49
  outliers final: 28
  residues processed: 177
  average time/residue: 0.0832
  time to fit residues: 20.0059
Evaluate side-chains
  158 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 124
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  458 GLN
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  627 LYS
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  751 VAL
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  884 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 38 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 1 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 50 optimal weight:    9.9990
   chunk 90 optimal weight:    6.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A  53 HIS
A 140 HIS
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 114 GLN
** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.120050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.093838 restraints weight = 22749.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 4.34
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   7777  Z= 0.184
  Angle     :  0.685  15.578  10534  Z= 0.347
  Chirality :  0.044   0.215   1243
  Planarity :  0.005   0.073   1327
  Dihedral  :  9.001 126.681   1089
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 14.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 30.25 %
    Favored  : 62.75 %
  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:  0.18 (0.26), residues: 987
  helix:  0.94 (0.23), residues: 483
  sheet: -0.83 (0.45), residues: 124
  loop : -0.50 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 760 
 TYR   0.016   0.002   TYR A 618 
 PHE   0.025   0.002   PHE A 218 
 TRP   0.029   0.003   TRP A 766 
 HIS   0.004   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 7776)
  covalent geometry    : angle       0.68460 (10532)
  SS BOND              : bond        0.00279 (    1)
  SS BOND              : angle       1.20404 (    2)
  hydrogen bonds       : bond        0.04184 (  423)
  hydrogen bonds       : angle       4.88740 ( 1293)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 123
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 MET cc_start: 0.7488 (mpp) cc_final: 0.7241 (mpp)
REVERT: A  167 ASP cc_start: 0.5598 (OUTLIER) cc_final: 0.5254 (m-30)
REVERT: A  320 LEU cc_start: 0.8442 (tt) cc_final: 0.8099 (pp)
REVERT: A  339 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8022 (pt0)
REVERT: A  359 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: A  458 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7421 (tt0)
REVERT: A  570 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7545 (p)
REVERT: A  718 SER cc_start: 0.7679 (t) cc_final: 0.7466 (p)
REVERT: A  779 ILE cc_start: 0.8352 (mt) cc_final: 0.8117 (mt)
REVERT: A  803 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.6551 (tp)
REVERT: A  871 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7538 (pm20)
REVERT: C   78 ARG cc_start: 0.8134 (tpt-90) cc_final: 0.7888 (tpt90)
REVERT: C  115 MET cc_start: 0.8491 (mmp) cc_final: 0.7739 (tmm)
  outliers start: 59
  outliers final: 34
  residues processed: 173
  average time/residue: 0.0749
  time to fit residues: 17.9998
Evaluate side-chains
  154 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 114
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  458 GLN
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  562 SER
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  637 SER
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  751 VAL
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  111 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 16 optimal weight:   20.0000
   chunk 80 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 91 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0470
   chunk 61 optimal weight:    0.0970
   chunk 59 optimal weight:    0.9990
   chunk 36 optimal weight:    0.5980
   chunk 39 optimal weight:    7.9990
   chunk 1 optimal weight:    0.1980
   overall best weight:    0.3878

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
A 724 ASN
** C  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 151 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 = 0.4297 r_free = 0.4297 target = 0.123376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.097199 restraints weight = 22221.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 4.36
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.3685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7777  Z= 0.124
  Angle     :  0.663  16.936  10534  Z= 0.330
  Chirality :  0.043   0.260   1243
  Planarity :  0.005   0.056   1327
  Dihedral  :  8.689 121.604   1088
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 31.32 %
    Favored  : 62.99 %
  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:  0.39 (0.27), residues: 987
  helix:  1.18 (0.23), residues: 483
  sheet: -1.04 (0.43), residues: 140
  loop : -0.31 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 760 
 TYR   0.015   0.001   TYR C 148 
 PHE   0.034   0.002   PHE C  80 
 TRP   0.034   0.002   TRP A 766 
 HIS   0.004   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 7776)
  covalent geometry    : angle       0.66320 (10532)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.49901 (    2)
  hydrogen bonds       : bond        0.03802 (  423)
  hydrogen bonds       : angle       4.69259 ( 1293)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 134
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8454 (mm110) cc_final: 0.8127 (tm-30)
REVERT: A   50 GLU cc_start: 0.3193 (OUTLIER) cc_final: 0.2989 (tt0)
REVERT: A   63 PHE cc_start: 0.6860 (OUTLIER) cc_final: 0.5459 (p90)
REVERT: A   85 MET cc_start: 0.7678 (mpp) cc_final: 0.7373 (mpp)
REVERT: A  101 ASP cc_start: 0.3221 (m-30) cc_final: 0.2786 (m-30)
REVERT: A  167 ASP cc_start: 0.5406 (OUTLIER) cc_final: 0.5088 (m-30)
REVERT: A  320 LEU cc_start: 0.8339 (tt) cc_final: 0.8043 (pp)
REVERT: A  339 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8111 (pt0)
REVERT: A  538 PHE cc_start: 0.7682 (t80) cc_final: 0.7450 (t80)
REVERT: A  718 SER cc_start: 0.7712 (t) cc_final: 0.7474 (p)
REVERT: A  871 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7457 (pm20)
REVERT: C  115 MET cc_start: 0.8476 (mmp) cc_final: 0.7686 (tmm)
REVERT: C  127 TYR cc_start: 0.8618 (m-10) cc_final: 0.8364 (m-10)
  outliers start: 48
  outliers final: 23
  residues processed: 168
  average time/residue: 0.0864
  time to fit residues: 19.4805
Evaluate side-chains
  148 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 120
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 GLU
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  562 SER
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  637 SER
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain C residue  112 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 67 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 3 optimal weight:    8.9990
   chunk 34 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 91 optimal weight:    0.5980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A  53 HIS
A 140 HIS
A 249 GLN
** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.120272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.095095 restraints weight = 22847.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.3759 rms_B_bonded: 4.36
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.3956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   7777  Z= 0.152
  Angle     :  0.706  16.884  10534  Z= 0.348
  Chirality :  0.043   0.150   1243
  Planarity :  0.005   0.054   1327
  Dihedral  :  8.695 123.302   1088
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 32.03 %
    Favored  : 61.92 %
  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:  0.35 (0.26), residues: 987
  helix:  1.18 (0.23), residues: 484
  sheet: -0.87 (0.43), residues: 133
  loop : -0.50 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  78 
 TYR   0.010   0.001   TYR A 618 
 PHE   0.038   0.002   PHE C  80 
 TRP   0.034   0.002   TRP A 766 
 HIS   0.004   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7776)
  covalent geometry    : angle       0.70611 (10532)
  SS BOND              : bond        0.00008 (    1)
  SS BOND              : angle       0.70074 (    2)
  hydrogen bonds       : bond        0.03890 (  423)
  hydrogen bonds       : angle       4.72625 ( 1293)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 125
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.5532 (p90)
REVERT: A   85 MET cc_start: 0.7673 (mpp) cc_final: 0.7354 (mpp)
REVERT: A  131 LEU cc_start: 0.8105 (tp) cc_final: 0.7817 (tp)
REVERT: A  167 ASP cc_start: 0.5621 (OUTLIER) cc_final: 0.5294 (m-30)
REVERT: A  320 LEU cc_start: 0.8351 (tt) cc_final: 0.8080 (pp)
REVERT: A  339 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8134 (pt0)
REVERT: A  496 LYS cc_start: 0.9427 (mmmt) cc_final: 0.9185 (tppt)
REVERT: A  538 PHE cc_start: 0.7648 (t80) cc_final: 0.7363 (t80)
REVERT: A  570 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7429 (p)
REVERT: A  718 SER cc_start: 0.7781 (t) cc_final: 0.7478 (p)
REVERT: A  761 LYS cc_start: 0.7323 (tmtt) cc_final: 0.7081 (tmtt)
REVERT: A  779 ILE cc_start: 0.8313 (mt) cc_final: 0.8053 (mt)
REVERT: A  803 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6558 (tp)
REVERT: A  871 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7529 (pm20)
REVERT: C  113 LEU cc_start: 0.7975 (mt) cc_final: 0.7750 (mt)
REVERT: C  115 MET cc_start: 0.8369 (mmp) cc_final: 0.7254 (tmm)
  outliers start: 51
  outliers final: 32
  residues processed: 166
  average time/residue: 0.0768
  time to fit residues: 17.6699
Evaluate side-chains
  154 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 116
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  562 SER
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  637 SER
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  751 VAL
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  112 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 95 optimal weight:    9.9990
   chunk 19 optimal weight:   10.0000
   chunk 90 optimal weight:   20.0000
   chunk 2 optimal weight:    9.9990
   chunk 14 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 730 ASN
** C 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.114492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.089027 restraints weight = 23047.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 4.20
r_work: 0.3480 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.4553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079   7777  Z= 0.267
  Angle     :  0.790  17.973  10534  Z= 0.402
  Chirality :  0.047   0.229   1243
  Planarity :  0.006   0.061   1327
  Dihedral  :  8.961 132.616   1088
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 19.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  7.59 %
    Allowed  : 30.25 %
    Favored  : 62.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.03 (0.26), residues: 987
  helix:  0.79 (0.23), residues: 484
  sheet: -0.80 (0.44), residues: 134
  loop : -0.67 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 796 
 TYR   0.017   0.002   TYR A 618 
 PHE   0.036   0.003   PHE C  80 
 TRP   0.037   0.003   TRP A 766 
 HIS   0.006   0.002   HIS A 140 

Details of bonding type rmsd
  covalent geometry    : bond        0.00612 ( 7776)
  covalent geometry    : angle       0.78950 (10532)
  SS BOND              : bond        0.00291 (    1)
  SS BOND              : angle       0.85402 (    2)
  hydrogen bonds       : bond        0.04717 (  423)
  hydrogen bonds       : angle       5.10125 ( 1293)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 122
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8384 (tm-30)
REVERT: A   85 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7801 (mpp)
REVERT: A  320 LEU cc_start: 0.8681 (tt) cc_final: 0.8323 (pp)
REVERT: A  339 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8180 (pt0)
REVERT: A  458 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7515 (tt0)
REVERT: A  496 LYS cc_start: 0.9531 (mmmt) cc_final: 0.9286 (tppt)
REVERT: A  538 PHE cc_start: 0.7942 (t80) cc_final: 0.7571 (t80)
REVERT: A  641 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.7080 (ttp)
REVERT: A  779 ILE cc_start: 0.8510 (mt) cc_final: 0.8278 (mt)
REVERT: A  871 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7649 (pm20)
REVERT: C  113 LEU cc_start: 0.8298 (mt) cc_final: 0.7964 (mt)
REVERT: C  115 MET cc_start: 0.8582 (mmp) cc_final: 0.7053 (tmm)
  outliers start: 64
  outliers final: 47
  residues processed: 173
  average time/residue: 0.0802
  time to fit residues: 18.9769
Evaluate side-chains
  167 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 115
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  458 GLN
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  562 SER
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  637 SER
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  751 VAL
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  825 SER
Chi-restraints excluded: chain A residue  832 SER
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  894 ILE
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  112 TYR
Chi-restraints excluded: chain C residue  148 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 19 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 89 optimal weight:   30.0000
   chunk 16 optimal weight:    0.0040
   chunk 92 optimal weight:   20.0000
   chunk 44 optimal weight:    6.9990
   chunk 67 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.9598

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
A 140 HIS
A 249 GLN
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.115475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.090660 restraints weight = 23201.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3688 rms_B_bonded: 4.41
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   7777  Z= 0.183
  Angle     :  0.747  18.440  10534  Z= 0.373
  Chirality :  0.044   0.166   1243
  Planarity :  0.005   0.056   1327
  Dihedral  :  8.906 129.498   1088
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 31.20 %
    Favored  : 62.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.14 (0.27), residues: 987
  helix:  0.99 (0.23), residues: 484
  sheet: -0.80 (0.44), residues: 134
  loop : -0.64 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 224 
 TYR   0.013   0.001   TYR C 148 
 PHE   0.029   0.002   PHE C  80 
 TRP   0.040   0.003   TRP A 766 
 HIS   0.004   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 7776)
  covalent geometry    : angle       0.74747 (10532)
  SS BOND              : bond        0.00145 (    1)
  SS BOND              : angle       0.66316 (    2)
  hydrogen bonds       : bond        0.04268 (  423)
  hydrogen bonds       : angle       4.90896 ( 1293)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 118
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8697 (mm110) cc_final: 0.8377 (tm-30)
REVERT: A   85 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7313 (mpp)
REVERT: A  320 LEU cc_start: 0.8414 (tt) cc_final: 0.8192 (pp)
REVERT: A  339 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8079 (pt0)
REVERT: A  458 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7449 (tt0)
REVERT: A  496 LYS cc_start: 0.9515 (mmmt) cc_final: 0.9259 (tppt)
REVERT: A  681 ASP cc_start: 0.7748 (t0) cc_final: 0.7536 (p0)
REVERT: A  778 LYS cc_start: 0.8273 (tppp) cc_final: 0.7925 (mtmm)
REVERT: A  779 ILE cc_start: 0.8435 (mt) cc_final: 0.8154 (mt)
REVERT: A  871 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7560 (pm20)
REVERT: C  113 LEU cc_start: 0.8456 (mt) cc_final: 0.8235 (mt)
REVERT: C  115 MET cc_start: 0.8362 (mmp) cc_final: 0.6958 (tmm)
  outliers start: 55
  outliers final: 44
  residues processed: 161
  average time/residue: 0.0867
  time to fit residues: 18.7745
Evaluate side-chains
  160 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 112
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  458 GLN
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  562 SER
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  637 SER
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  751 VAL
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  783 SER
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  825 SER
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  894 ILE
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  112 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 85 optimal weight:    6.9990
   chunk 73 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0570
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 4 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.9102

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.117611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.092871 restraints weight = 22519.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3725 rms_B_bonded: 4.47
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.4673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   7777  Z= 0.145
  Angle     :  0.737  18.645  10534  Z= 0.366
  Chirality :  0.044   0.159   1243
  Planarity :  0.005   0.054   1327
  Dihedral  :  8.851 124.690   1088
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 32.03 %
    Favored  : 62.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.28 (0.27), residues: 987
  helix:  1.19 (0.23), residues: 479
  sheet: -0.84 (0.43), residues: 131
  loop : -0.65 (0.32), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 224 
 TYR   0.022   0.001   TYR C 148 
 PHE   0.044   0.002   PHE C 100 
 TRP   0.043   0.003   TRP A 766 
 HIS   0.003   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 7776)
  covalent geometry    : angle       0.73655 (10532)
  SS BOND              : bond        0.00093 (    1)
  SS BOND              : angle       0.46702 (    2)
  hydrogen bonds       : bond        0.03988 (  423)
  hydrogen bonds       : angle       4.79777 ( 1293)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 123
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8692 (mm110) cc_final: 0.8357 (tm-30)
REVERT: A   85 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.7362 (mpp)
REVERT: A  131 LEU cc_start: 0.7969 (tp) cc_final: 0.7625 (tp)
REVERT: A  294 MET cc_start: 0.8347 (ttm) cc_final: 0.8006 (ttm)
REVERT: A  339 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8066 (pt0)
REVERT: A  496 LYS cc_start: 0.9504 (mmmt) cc_final: 0.9239 (tppt)
REVERT: A  778 LYS cc_start: 0.8154 (tppp) cc_final: 0.7832 (mtmm)
REVERT: A  779 ILE cc_start: 0.8395 (mt) cc_final: 0.8095 (mt)
REVERT: A  871 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7514 (pm20)
  outliers start: 48
  outliers final: 40
  residues processed: 158
  average time/residue: 0.0816
  time to fit residues: 17.5199
Evaluate side-chains
  162 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 119
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  249 GLN
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  562 SER
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  637 SER
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  751 VAL
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  791 LEU
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  148 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 18 optimal weight:    0.1980
   chunk 1 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 3 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.118426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.093295 restraints weight = 22312.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 4.24
r_work: 0.3572 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.3572
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.4759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   7777  Z= 0.142
  Angle     :  0.765  18.788  10534  Z= 0.376
  Chirality :  0.044   0.201   1243
  Planarity :  0.004   0.055   1327
  Dihedral  :  8.846 122.296   1088
  Min Nonbonded Distance : 2.082

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 32.98 %
    Favored  : 62.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.38 (0.27), residues: 987
  helix:  1.25 (0.23), residues: 479
  sheet: -0.76 (0.44), residues: 130
  loop : -0.57 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 224 
 TYR   0.016   0.001   TYR C 148 
 PHE   0.036   0.002   PHE C 100 
 TRP   0.045   0.003   TRP A 766 
 HIS   0.003   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 7776)
  covalent geometry    : angle       0.76523 (10532)
  SS BOND              : bond        0.00013 (    1)
  SS BOND              : angle       0.46786 (    2)
  hydrogen bonds       : bond        0.03963 (  423)
  hydrogen bonds       : angle       4.73640 ( 1293)

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 124
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8768 (mm110) cc_final: 0.8381 (tm-30)
REVERT: A   85 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7652 (mpp)
REVERT: A  131 LEU cc_start: 0.7988 (tp) cc_final: 0.7669 (tp)
REVERT: A  339 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8138 (pt0)
REVERT: A  417 ARG cc_start: 0.8924 (ttt-90) cc_final: 0.8549 (ttp80)
REVERT: A  496 LYS cc_start: 0.9526 (mmmt) cc_final: 0.9293 (tppt)
REVERT: A  661 MET cc_start: 0.8085 (mmm) cc_final: 0.7873 (tpp)
REVERT: A  691 GLU cc_start: 0.7770 (pp20) cc_final: 0.7432 (pp20)
REVERT: A  778 LYS cc_start: 0.8448 (tppp) cc_final: 0.7862 (mtmm)
REVERT: A  779 ILE cc_start: 0.8424 (mt) cc_final: 0.8153 (mt)
REVERT: A  871 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7625 (pm20)
REVERT: C  115 MET cc_start: 0.8650 (mmm) cc_final: 0.6770 (tmm)
  outliers start: 41
  outliers final: 36
  residues processed: 155
  average time/residue: 0.0893
  time to fit residues: 18.6213
Evaluate side-chains
  159 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 120
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue   85 MET
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  331 ILE
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  517 MET
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  562 SER
Chi-restraints excluded: chain A residue  566 ILE
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  637 SER
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  740 ILE
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  783 SER
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  148 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 42 optimal weight:    0.0570
   chunk 61 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 89 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 98 optimal weight:   20.0000
   chunk 88 optimal weight:    0.0970
   overall best weight:    0.5696

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

Flipped N/Q/H residues before XYZ refinement:
A  53 HIS
A 249 GLN
** A 512 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 747 GLN
** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.119387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.094235 restraints weight = 22480.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 4.30
r_work: 0.3590 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.4850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7777  Z= 0.136
  Angle     :  0.760  18.601  10534  Z= 0.372
  Chirality :  0.043   0.176   1243
  Planarity :  0.004   0.055   1327
  Dihedral  :  8.795 118.664   1088
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 32.98 %
    Favored  : 61.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.27), residues: 987
  helix:  1.27 (0.23), residues: 480
  sheet: -0.70 (0.43), residues: 130
  loop : -0.54 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 760 
 TYR   0.015   0.001   TYR C 148 
 PHE   0.040   0.002   PHE C 100 
 TRP   0.043   0.003   TRP A 766 
 HIS   0.004   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 7776)
  covalent geometry    : angle       0.76033 (10532)
  SS BOND              : bond        0.00119 (    1)
  SS BOND              : angle       0.57596 (    2)
  hydrogen bonds       : bond        0.03797 (  423)
  hydrogen bonds       : angle       4.64976 ( 1293)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1654.81 seconds
wall clock time: 29 minutes 7.31 seconds (1747.31 seconds total)