Starting phenix.real_space_refine
on Wed Mar 12 11:27:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yaj_33714/03_2025/7yaj_33714.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yaj_33714/03_2025/7yaj_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yaj_33714/03_2025/7yaj_33714.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yaj_33714/03_2025/7yaj_33714.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yaj_33714/03_2025/7yaj_33714.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yaj_33714/03_2025/7yaj_33714.cif"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.020
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: 4.97, per 1000 atoms: 0.65
  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: 2.19
  Conformation dependent library (CDL) restraints added in 910.6 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: 0.93
  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: 2.99

  Time building geometry restraints manager: 2.54 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:             164.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.000
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  189.640
-------------------------------------------------------------------------------
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   7776  Z= 0.339
  Angle     :  0.947  13.944  10532  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.24), 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
 TRP   0.042   0.002   TRP C 149 
 HIS   0.008   0.001   HIS A 467 
 PHE   0.020   0.002   PHE A 383 
 TYR   0.027   0.003   TYR C 143 
 ARG   0.005   0.001   ARG C  99 

*********************** 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  : 0.796 
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: 0.3003 (m-30) cc_final: 0.2694 (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: 0.2119
  time to fit residues: 54.3817
Evaluate side-chains
  141 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 136
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
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 83 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    5.9990
   chunk 50 optimal weight:    9.9990
   chunk 40 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 47 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   overall best weight:    1.8184

-------------------------------------------------------------------------------
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 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 506 GLN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.122177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.095365 restraints weight = 22444.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3761 rms_B_bonded: 4.35
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7231
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   7776  Z= 0.266
  Angle     :  0.689   9.463  10532  Z= 0.356
  Chirality :  0.043   0.156   1243
  Planarity :  0.006   0.067   1327
  Dihedral  :  9.563 125.131   1096
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 30.13 %
    Favored  : 64.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.26), residues: 987
  helix:  0.52 (0.23), residues: 482
  sheet: -0.83 (0.45), residues: 130
  loop : -0.63 (0.31), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 766 
 HIS   0.009   0.002   HIS A  53 
 PHE   0.028   0.002   PHE C 100 
 TYR   0.025   0.002   TYR A 618 
 ARG   0.006   0.001   ARG C  99 

*********************** 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
  187 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 144
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 MET cc_start: 0.7532 (mpp) cc_final: 0.7092 (mpp)
REVERT: A  129 GLU cc_start: 0.8924 (tp30) cc_final: 0.8691 (tm-30)
REVERT: A  131 LEU cc_start: 0.7934 (tp) cc_final: 0.7721 (tp)
REVERT: A  167 ASP cc_start: 0.5468 (OUTLIER) cc_final: 0.5126 (m-30)
REVERT: A  320 LEU cc_start: 0.8460 (tt) cc_final: 0.8065 (pp)
REVERT: A  339 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7702 (pt0)
REVERT: A  412 ASN cc_start: 0.7142 (m-40) cc_final: 0.6773 (m110)
REVERT: A  444 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8968 (pm20)
REVERT: A  677 LEU cc_start: 0.7821 (pt) cc_final: 0.7251 (tp)
REVERT: A  681 ASP cc_start: 0.7488 (p0) cc_final: 0.7216 (p0)
REVERT: A  803 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6432 (tp)
REVERT: C   51 LEU cc_start: 0.7720 (tt) cc_final: 0.7233 (mp)
REVERT: C   99 ARG cc_start: 0.7812 (ptt-90) cc_final: 0.5744 (ttp80)
  outliers start: 43
  outliers final: 20
  residues processed: 178
  average time/residue: 0.2080
  time to fit residues: 49.6500
Evaluate side-chains
  150 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  409 CYS
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  444 GLN
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  582 SER
Chi-restraints excluded: chain A residue  586 LEU
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  740 ILE
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  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 19 optimal weight:    9.9990
   chunk 68 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 41 optimal weight:    9.9990
   chunk 8 optimal weight:    3.9990
   chunk 52 optimal weight:    0.3980
   chunk 94 optimal weight:    7.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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**
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.122738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.096145 restraints weight = 22764.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 4.37
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7776  Z= 0.208
  Angle     :  0.615   7.419  10532  Z= 0.322
  Chirality :  0.042   0.151   1243
  Planarity :  0.005   0.062   1327
  Dihedral  :  9.047 123.291   1091
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 13.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 30.01 %
    Favored  : 64.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.26), residues: 987
  helix:  0.92 (0.23), residues: 483
  sheet: -0.76 (0.45), residues: 128
  loop : -0.61 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 766 
 HIS   0.005   0.001   HIS C  86 
 PHE   0.022   0.002   PHE A 241 
 TYR   0.016   0.001   TYR C 148 
 ARG   0.008   0.001   ARG C  78 

*********************** 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
  186 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 141
  time to evaluate  : 0.824 
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   50 GLU cc_start: 0.3368 (OUTLIER) cc_final: 0.3165 (tt0)
REVERT: A  101 ASP cc_start: 0.2704 (m-30) cc_final: 0.2442 (m-30)
REVERT: A  129 GLU cc_start: 0.8946 (tp30) cc_final: 0.8732 (tm-30)
REVERT: A  167 ASP cc_start: 0.5442 (OUTLIER) cc_final: 0.5140 (m-30)
REVERT: A  320 LEU cc_start: 0.8448 (tt) cc_final: 0.8072 (pp)
REVERT: A  339 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8072 (pt0)
REVERT: A  359 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7592 (tm-30)
REVERT: A  412 ASN cc_start: 0.7337 (m-40) cc_final: 0.6989 (m110)
REVERT: A  437 MET cc_start: 0.8252 (tpt) cc_final: 0.7981 (tpt)
REVERT: A  803 ILE cc_start: 0.6683 (OUTLIER) cc_final: 0.6386 (tp)
REVERT: A  871 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7450 (pm20)
REVERT: C   51 LEU cc_start: 0.7853 (tt) cc_final: 0.7130 (mp)
  outliers start: 45
  outliers final: 21
  residues processed: 177
  average time/residue: 0.2191
  time to fit residues: 51.8216
Evaluate side-chains
  151 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
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  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  426 THR
Chi-restraints excluded: chain A residue  430 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  550 THR
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  740 ILE
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  871 GLU
Chi-restraints excluded: chain A residue  894 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 17 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 28 optimal weight:    0.5980
   chunk 30 optimal weight:    7.9990
   chunk 62 optimal weight:    0.0870
   chunk 71 optimal weight:    5.9990
   chunk 56 optimal weight:    0.2980
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.5962

-------------------------------------------------------------------------------
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 ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.120743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.094553 restraints weight = 22506.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3749 rms_B_bonded: 4.34
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   7776  Z= 0.241
  Angle     :  0.638   9.825  10532  Z= 0.331
  Chirality :  0.043   0.203   1243
  Planarity :  0.006   0.077   1327
  Dihedral  :  8.869 125.514   1088
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 30.25 %
    Favored  : 63.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.26), residues: 987
  helix:  1.07 (0.23), residues: 481
  sheet: -0.76 (0.45), residues: 124
  loop : -0.55 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 766 
 HIS   0.004   0.001   HIS C  86 
 PHE   0.014   0.002   PHE C  80 
 TYR   0.014   0.001   TYR A 618 
 ARG   0.009   0.001   ARG C  99 

*********************** 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
  179 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 125
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 GLU cc_start: 0.8941 (tp30) cc_final: 0.8680 (tm-30)
REVERT: A  167 ASP cc_start: 0.5614 (OUTLIER) cc_final: 0.5297 (m-30)
REVERT: A  320 LEU cc_start: 0.8435 (tt) cc_final: 0.8092 (pp)
REVERT: A  339 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8022 (pt0)
REVERT: A  359 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7706 (tm-30)
REVERT: A  458 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7476 (tt0)
REVERT: A  570 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7411 (p)
REVERT: A  677 LEU cc_start: 0.8133 (pt) cc_final: 0.7597 (pt)
REVERT: A  718 SER cc_start: 0.7764 (t) cc_final: 0.7542 (p)
REVERT: A  803 ILE cc_start: 0.6766 (OUTLIER) cc_final: 0.6465 (tp)
REVERT: A  871 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7507 (pm20)
REVERT: C  115 MET cc_start: 0.8529 (mmp) cc_final: 0.7748 (tmm)
  outliers start: 54
  outliers final: 33
  residues processed: 170
  average time/residue: 0.2179
  time to fit residues: 50.6991
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  : 1.766 
-------------------------------------------------------------------------------
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  426 THR
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  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  699 ILE
Chi-restraints excluded: chain A residue  715 THR
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  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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 89 optimal weight:   40.0000
   chunk 50 optimal weight:    9.9990
   chunk 88 optimal weight:    0.0070
   chunk 0 optimal weight:    9.9990
   chunk 14 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   chunk 38 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    1.1602

-------------------------------------------------------------------------------
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 724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 114 GLN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.120459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.093841 restraints weight = 22682.841|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 4.28
r_work: 0.3590 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.3700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7776  Z= 0.210
  Angle     :  0.624   9.552  10532  Z= 0.323
  Chirality :  0.043   0.313   1243
  Planarity :  0.005   0.060   1327
  Dihedral  :  8.763 124.491   1088
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 30.60 %
    Favored  : 63.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.26), residues: 987
  helix:  1.20 (0.23), residues: 483
  sheet: -0.83 (0.44), residues: 126
  loop : -0.59 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP A 766 
 HIS   0.004   0.001   HIS C  86 
 PHE   0.033   0.002   PHE C  80 
 TYR   0.013   0.001   TYR C 148 
 ARG   0.005   0.000   ARG A 796 

*********************** 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
  178 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 125
  time to evaluate  : 0.887 
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   85 MET cc_start: 0.8055 (mpp) cc_final: 0.7613 (mpp)
REVERT: A  167 ASP cc_start: 0.5783 (OUTLIER) cc_final: 0.5495 (m-30)
REVERT: A  320 LEU cc_start: 0.8555 (tt) cc_final: 0.8177 (pp)
REVERT: A  339 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8297 (pt0)
REVERT: A  437 MET cc_start: 0.8617 (tpt) cc_final: 0.8242 (tpt)
REVERT: A  458 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7529 (tt0)
REVERT: A  538 PHE cc_start: 0.7719 (t80) cc_final: 0.7468 (t80)
REVERT: A  570 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7477 (p)
REVERT: A  687 SER cc_start: 0.9183 (m) cc_final: 0.8931 (p)
REVERT: A  779 ILE cc_start: 0.8385 (mt) cc_final: 0.8104 (mt)
REVERT: A  803 ILE cc_start: 0.6797 (OUTLIER) cc_final: 0.6478 (tp)
REVERT: A  871 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7676 (pm20)
REVERT: C   51 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7492 (tt)
REVERT: C  115 MET cc_start: 0.8221 (mmp) cc_final: 0.7431 (tmm)
REVERT: C  127 TYR cc_start: 0.8650 (m-10) cc_final: 0.8317 (m-10)
  outliers start: 53
  outliers final: 32
  residues processed: 166
  average time/residue: 0.1899
  time to fit residues: 43.2472
Evaluate side-chains
  155 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  188 LEU
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  426 THR
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  566 ILE
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  582 SER
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  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  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  848 VAL
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   51 LEU
Chi-restraints excluded: chain C residue  111 VAL
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 53 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 72 optimal weight:    7.9990
   chunk 83 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 6 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
A  53 HIS
A 140 HIS
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 724 ASN
A 730 ASN
** C 114 GLN ** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.118675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.093573 restraints weight = 22408.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 4.26
r_work: 0.3552 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.4049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7776  Z= 0.262
  Angle     :  0.673  14.317  10532  Z= 0.339
  Chirality :  0.042   0.163   1243
  Planarity :  0.005   0.060   1327
  Dihedral  :  8.684 126.357   1088
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  7.12 %
    Allowed  : 30.72 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.26), residues: 987
  helix:  1.19 (0.23), residues: 482
  sheet: -0.94 (0.43), residues: 132
  loop : -0.67 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.003   TRP A 766 
 HIS   0.005   0.001   HIS A  53 
 PHE   0.023   0.002   PHE C  80 
 TYR   0.011   0.001   TYR A 618 
 ARG   0.005   0.001   ARG A 796 

*********************** 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
  183 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 123
  time to evaluate  : 1.103 
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: 0.8635 (mm110) cc_final: 0.8279 (tm-30)
REVERT: A   63 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.5652 (p90)
REVERT: A   85 MET cc_start: 0.8088 (mpp) cc_final: 0.7643 (mpp)
REVERT: A  167 ASP cc_start: 0.6041 (OUTLIER) cc_final: 0.5765 (m-30)
REVERT: A  243 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7706 (pm20)
REVERT: A  320 LEU cc_start: 0.8611 (tt) cc_final: 0.8233 (pp)
REVERT: A  339 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8209 (pt0)
REVERT: A  458 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.7501 (tt0)
REVERT: A  496 LYS cc_start: 0.9463 (mmmt) cc_final: 0.9236 (tppt)
REVERT: A  570 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.7658 (p)
REVERT: A  687 SER cc_start: 0.9146 (m) cc_final: 0.8911 (p)
REVERT: A  779 ILE cc_start: 0.8445 (mt) cc_final: 0.8170 (mt)
REVERT: A  803 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6646 (tp)
REVERT: A  871 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7593 (pm20)
REVERT: C   51 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7627 (tt)
REVERT: C  113 LEU cc_start: 0.8003 (mt) cc_final: 0.7798 (mt)
REVERT: C  115 MET cc_start: 0.8418 (mmp) cc_final: 0.7281 (tmm)
  outliers start: 60
  outliers final: 37
  residues processed: 172
  average time/residue: 0.3324
  time to fit residues: 78.6226
Evaluate side-chains
  158 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 112
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  243 GLU
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  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  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  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  686 MET
Chi-restraints excluded: chain A residue  715 THR
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  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  825 SER
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  894 ILE
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue   84 ILE
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 76 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 87 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   chunk 84 optimal weight:    5.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
C 114 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.119433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.093868 restraints weight = 22433.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3729 rms_B_bonded: 4.34
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7302
moved from start:          0.4159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7776  Z= 0.205
  Angle     :  0.646  12.441  10532  Z= 0.331
  Chirality :  0.043   0.159   1243
  Planarity :  0.005   0.060   1327
  Dihedral  :  8.561 123.288   1088
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 13.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 31.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.26), residues: 987
  helix:  1.29 (0.23), residues: 482
  sheet: -0.89 (0.43), residues: 135
  loop : -0.64 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 766 
 HIS   0.003   0.001   HIS C  86 
 PHE   0.038   0.002   PHE C  80 
 TYR   0.015   0.001   TYR C 148 
 ARG   0.012   0.001   ARG A 760 

*********************** 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
  185 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 126
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8478 (mm110) cc_final: 0.8206 (tm-30)
REVERT: A   63 PHE cc_start: 0.6809 (OUTLIER) cc_final: 0.5441 (p90)
REVERT: A   85 MET cc_start: 0.7570 (mpp) cc_final: 0.7215 (mpp)
REVERT: A  167 ASP cc_start: 0.5773 (OUTLIER) cc_final: 0.5474 (m-30)
REVERT: A  243 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7592 (pm20)
REVERT: A  320 LEU cc_start: 0.8390 (tt) cc_final: 0.8131 (pp)
REVERT: A  339 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8112 (pt0)
REVERT: A  458 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7446 (tt0)
REVERT: A  496 LYS cc_start: 0.9441 (mmmt) cc_final: 0.9193 (tppt)
REVERT: A  570 THR cc_start: 0.7978 (OUTLIER) cc_final: 0.7339 (p)
REVERT: A  687 SER cc_start: 0.9252 (m) cc_final: 0.9032 (p)
REVERT: A  691 GLU cc_start: 0.7491 (pp20) cc_final: 0.7215 (pp20)
REVERT: A  778 LYS cc_start: 0.8176 (tppp) cc_final: 0.7845 (mtmm)
REVERT: A  779 ILE cc_start: 0.8389 (mt) cc_final: 0.8092 (mt)
REVERT: A  803 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6655 (tp)
REVERT: A  871 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7461 (pm20)
REVERT: C  115 MET cc_start: 0.8072 (mmp) cc_final: 0.6930 (ppp)
  outliers start: 59
  outliers final: 41
  residues processed: 171
  average time/residue: 0.2187
  time to fit residues: 50.7782
Evaluate side-chains
  166 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 117
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   63 PHE
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  247 MET
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  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  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  559 LEU
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  631 SER
Chi-restraints excluded: chain A residue  637 SER
Chi-restraints excluded: chain A residue  686 MET
Chi-restraints excluded: chain A residue  715 THR
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  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  879 LEU
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 51 optimal weight:    0.0970
   chunk 24 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.7778

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

Flipped N/Q/H residues before XYZ refinement:
A  53 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.120359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.095732 restraints weight = 22543.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 4.44
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.4311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   7776  Z= 0.192
  Angle     :  0.662  12.111  10532  Z= 0.333
  Chirality :  0.042   0.156   1243
  Planarity :  0.005   0.059   1327
  Dihedral  :  8.439 120.786   1088
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 31.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.27), residues: 987
  helix:  1.41 (0.23), residues: 482
  sheet: -0.68 (0.45), residues: 131
  loop : -0.65 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP A 766 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.030   0.002   PHE C  80 
 TYR   0.014   0.001   TYR C 148 
 ARG   0.011   0.000   ARG A 760 

*********************** 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
  184 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 127
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8544 (mm110) cc_final: 0.8171 (tm-30)
REVERT: A   63 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.5586 (p90)
REVERT: A   84 ILE cc_start: 0.8022 (mm) cc_final: 0.7821 (mm)
REVERT: A   85 MET cc_start: 0.7615 (mpp) cc_final: 0.7222 (mpp)
REVERT: A  131 LEU cc_start: 0.8139 (tp) cc_final: 0.7929 (tp)
REVERT: A  167 ASP cc_start: 0.5780 (OUTLIER) cc_final: 0.5451 (m-30)
REVERT: A  243 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7587 (pm20)
REVERT: A  320 LEU cc_start: 0.8320 (tt) cc_final: 0.8102 (pp)
REVERT: A  339 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8101 (pt0)
REVERT: A  417 ARG cc_start: 0.8808 (ttt-90) cc_final: 0.8402 (ttp80)
REVERT: A  458 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7376 (tt0)
REVERT: A  496 LYS cc_start: 0.9469 (mmmt) cc_final: 0.9229 (tppt)
REVERT: A  570 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7326 (p)
REVERT: A  687 SER cc_start: 0.9220 (m) cc_final: 0.8997 (p)
REVERT: A  691 GLU cc_start: 0.7464 (pp20) cc_final: 0.7147 (pp20)
REVERT: A  778 LYS cc_start: 0.8150 (tppp) cc_final: 0.7834 (mtmm)
REVERT: A  779 ILE cc_start: 0.8327 (mt) cc_final: 0.8035 (mt)
REVERT: A  803 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6524 (tp)
REVERT: A  853 MET cc_start: 0.7290 (tmm) cc_final: 0.6990 (tmm)
REVERT: A  871 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7432 (pm20)
REVERT: C   78 ARG cc_start: 0.7965 (tpt170) cc_final: 0.7191 (mmm-85)
REVERT: C  115 MET cc_start: 0.8177 (mmp) cc_final: 0.6826 (ppp)
REVERT: C  119 LYS cc_start: 0.9122 (mmtt) cc_final: 0.8914 (mmtt)
  outliers start: 57
  outliers final: 37
  residues processed: 173
  average time/residue: 0.2176
  time to fit residues: 50.2080
Evaluate side-chains
  166 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 121
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
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  175 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  243 GLU
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  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  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  559 LEU
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  631 SER
Chi-restraints excluded: chain A residue  637 SER
Chi-restraints excluded: chain A residue  686 MET
Chi-restraints excluded: chain A residue  715 THR
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  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   84 ILE
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  148 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 41 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9990
   overall best weight:    1.1186

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.119415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.094300 restraints weight = 22510.139|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 4.37
r_work: 0.3579 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.4481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   7776  Z= 0.210
  Angle     :  0.669  11.993  10532  Z= 0.337
  Chirality :  0.043   0.164   1243
  Planarity :  0.005   0.059   1327
  Dihedral  :  8.331 120.472   1088
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 31.20 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.27), residues: 987
  helix:  1.38 (0.23), residues: 481
  sheet: -0.63 (0.44), residues: 131
  loop : -0.64 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.003   TRP A 766 
 HIS   0.003   0.001   HIS C  86 
 PHE   0.029   0.002   PHE C  80 
 TYR   0.014   0.001   TYR C 148 
 ARG   0.012   0.001   ARG A 760 

*********************** 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
  174 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 123
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8666 (mm110) cc_final: 0.8263 (tm-30)
REVERT: A   63 PHE cc_start: 0.7082 (OUTLIER) cc_final: 0.5577 (p90)
REVERT: A   84 ILE cc_start: 0.8101 (mm) cc_final: 0.7881 (mm)
REVERT: A   85 MET cc_start: 0.8004 (mpp) cc_final: 0.7526 (mpp)
REVERT: A  131 LEU cc_start: 0.8094 (tp) cc_final: 0.7842 (tp)
REVERT: A  167 ASP cc_start: 0.5946 (OUTLIER) cc_final: 0.5683 (m-30)
REVERT: A  320 LEU cc_start: 0.8576 (tt) cc_final: 0.8254 (pp)
REVERT: A  339 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8176 (pt0)
REVERT: A  417 ARG cc_start: 0.8963 (ttt-90) cc_final: 0.8588 (ttp80)
REVERT: A  458 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7406 (tt0)
REVERT: A  496 LYS cc_start: 0.9480 (mmmt) cc_final: 0.9256 (tppt)
REVERT: A  570 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7593 (p)
REVERT: A  687 SER cc_start: 0.9210 (m) cc_final: 0.8991 (p)
REVERT: A  691 GLU cc_start: 0.7630 (pp20) cc_final: 0.7302 (pp20)
REVERT: A  778 LYS cc_start: 0.8436 (tppp) cc_final: 0.7860 (mtmm)
REVERT: A  779 ILE cc_start: 0.8418 (mt) cc_final: 0.8150 (mt)
REVERT: A  803 ILE cc_start: 0.6883 (OUTLIER) cc_final: 0.6536 (tp)
REVERT: A  871 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7564 (pm20)
REVERT: C   51 LEU cc_start: 0.7904 (mp) cc_final: 0.7212 (tt)
  outliers start: 51
  outliers final: 40
  residues processed: 164
  average time/residue: 0.2123
  time to fit residues: 46.6241
Evaluate side-chains
  161 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 114
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
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   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  175 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  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  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  559 LEU
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  631 SER
Chi-restraints excluded: chain A residue  637 SER
Chi-restraints excluded: chain A residue  715 THR
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  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  848 VAL
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 56 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 85 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 21 optimal weight:    9.9990
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.5188

-------------------------------------------------------------------------------
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 ** 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 = 0.4213 r_free = 0.4213 target = 0.118362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.093521 restraints weight = 22469.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3729 rms_B_bonded: 4.54
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
moved from start:          0.4627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   7776  Z= 0.240
  Angle     :  0.719  13.102  10532  Z= 0.360
  Chirality :  0.043   0.198   1243
  Planarity :  0.005   0.074   1327
  Dihedral  :  8.419 120.938   1088
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 14.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 31.55 %
    Favored  : 62.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.27), residues: 987
  helix:  1.32 (0.23), residues: 483
  sheet: -0.63 (0.44), residues: 131
  loop : -0.65 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP A 766 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.044   0.002   PHE C 100 
 TYR   0.013   0.001   TYR C 148 
 ARG   0.013   0.001   ARG A 760 

********************** 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
  164 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 111
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8687 (mm110) cc_final: 0.8344 (tm-30)
REVERT: A   63 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.5519 (p90)
REVERT: A   85 MET cc_start: 0.7590 (mpp) cc_final: 0.7227 (mpp)
REVERT: A  131 LEU cc_start: 0.8090 (tp) cc_final: 0.7885 (tp)
REVERT: A  167 ASP cc_start: 0.5920 (OUTLIER) cc_final: 0.5670 (m-30)
REVERT: A  339 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8020 (pt0)
REVERT: A  458 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7380 (tt0)
REVERT: A  496 LYS cc_start: 0.9490 (mmmt) cc_final: 0.9254 (tppt)
REVERT: A  570 THR cc_start: 0.8179 (OUTLIER) cc_final: 0.7569 (p)
REVERT: A  691 GLU cc_start: 0.7439 (pp20) cc_final: 0.7205 (pp20)
REVERT: A  778 LYS cc_start: 0.8198 (tppp) cc_final: 0.7856 (mtmm)
REVERT: A  779 ILE cc_start: 0.8403 (mt) cc_final: 0.8136 (mt)
REVERT: A  803 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6656 (tp)
REVERT: A  853 MET cc_start: 0.7319 (tmm) cc_final: 0.7035 (tmm)
REVERT: A  871 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7453 (pm20)
REVERT: C   51 LEU cc_start: 0.7764 (mp) cc_final: 0.7206 (tt)
REVERT: C  115 MET cc_start: 0.8466 (mmp) cc_final: 0.7180 (tmm)
  outliers start: 53
  outliers final: 42
  residues processed: 155
  average time/residue: 0.1975
  time to fit residues: 41.8135
Evaluate side-chains
  158 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 109
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
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   86 LEU
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   98 HIS
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  175 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  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  412 ASN
Chi-restraints excluded: chain A residue  426 THR
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  559 LEU
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  631 SER
Chi-restraints excluded: chain A residue  637 SER
Chi-restraints excluded: chain A residue  715 THR
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  798 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  825 SER
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  871 GLU
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 19 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 70 optimal weight:    0.8980
   chunk 96 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 249 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.118802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.094127 restraints weight = 22419.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 4.36
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.4719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   7776  Z= 0.225
  Angle     :  0.701  11.984  10532  Z= 0.351
  Chirality :  0.043   0.224   1243
  Planarity :  0.005   0.060   1327
  Dihedral  :  8.353 119.907   1088
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 31.32 %
    Favored  : 62.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.27), residues: 987
  helix:  1.30 (0.23), residues: 482
  sheet: -0.65 (0.44), residues: 131
  loop : -0.63 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP A 766 
 HIS   0.003   0.001   HIS C  86 
 PHE   0.041   0.002   PHE C 100 
 TYR   0.013   0.002   TYR C 127 
 ARG   0.012   0.001   ARG A 760 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4159.31 seconds
wall clock time: 75 minutes 29.49 seconds (4529.49 seconds total)