Starting phenix.real_space_refine
on Fri Jul 25 16:08:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yaj_33714/07_2025/7yaj_33714.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yaj_33714/07_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_33714/07_2025/7yaj_33714.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yaj_33714/07_2025/7yaj_33714.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yaj_33714/07_2025/7yaj_33714.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yaj_33714/07_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.08, per 1000 atoms: 0.66
  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: 2.42
  Conformation dependent library (CDL) restraints added in 973.5 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: 0.94
  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: 2.96

  Time building geometry restraints manager: 2.48 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 234
        2.70 -     3.25: 7495
        3.25 -     3.80: 13133
        3.80 -     4.35: 16135
        4.35 -     4.90: 26696
  Nonbonded interactions: 63693
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 742 "
            pdb="MN    MN A1002 "
     model   vdw
     2.150 2.320
  nonbonded pdb=" O   VAL A 303 "
            pdb="MN    MN A1002 "
     model   vdw
     2.275 2.320
  nonbonded pdb=" OE1 GLU A 513 "
            pdb=" OH  TYR C 143 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OG  SER A 456 "
            pdb=" O2A ACP A1001 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   SER C 145 "
            pdb=" OG  SER C 145 "
     model   vdw
     2.279 3.040
  ... (remaining 63688 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.690
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6647
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.090   7777  Z= 0.306
  Angle     :  0.947  13.944  10534  Z= 0.542
  Chirality :  0.054   0.306   1243
  Planarity :  0.009   0.149   1327
  Dihedral  : 18.800 124.004   2878
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 30.37 %
    Favored  : 67.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 

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

*********************** 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  : 0.949 
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: 0.2197
  time to fit residues: 56.3293
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  : 0.881 
-------------------------------------------------------------------------------
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   7777  Z= 0.185
  Angle     :  0.689   9.463  10534  Z= 0.357
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04563 (  423)
  hydrogen bonds       : angle       5.11417 ( 1293)
  SS BOND              : bond        0.00275 (    1)
  SS BOND              : angle       1.36326 (    2)
  covalent geometry    : bond        0.00413 ( 7776)
  covalent geometry    : angle       0.68915 (10532)

*********************** 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  : 1.069 
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: 0.3049
  time to fit residues: 72.9200
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  : 0.919 
-------------------------------------------------------------------------------
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:    0.9990
   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:    0.7984

-------------------------------------------------------------------------------
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
** 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 = 0.4290 r_free = 0.4290 target = 0.123269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.096770 restraints weight = 22701.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 4.35
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7777  Z= 0.135
  Angle     :  0.611   7.392  10534  Z= 0.319
  Chirality :  0.042   0.156   1243
  Planarity :  0.005   0.061   1327
  Dihedral  :  9.019 122.602   1091
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 30.25 %
    Favored  : 64.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.26), residues: 987
  helix:  0.92 (0.23), residues: 483
  sheet: -0.76 (0.45), residues: 128
  loop : -0.62 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 766 
 HIS   0.005   0.001   HIS C  86 
 PHE   0.019   0.002   PHE A 818 
 TYR   0.018   0.001   TYR C 148 
 ARG   0.006   0.001   ARG A 760 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04071 (  423)
  hydrogen bonds       : angle       4.79580 ( 1293)
  SS BOND              : bond        0.00239 (    1)
  SS BOND              : angle       1.02579 (    2)
  covalent geometry    : bond        0.00300 ( 7776)
  covalent geometry    : angle       0.61094 (10532)

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

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

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

  1974 Ramachandran restraints generated.
    987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 142
  time to evaluate  : 0.938 
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: 0.3253 (OUTLIER) cc_final: 0.3048 (tt0)
REVERT: A  101 ASP cc_start: 0.3134 (m-30) cc_final: 0.2710 (m-30)
REVERT: A  129 GLU cc_start: 0.8941 (tp30) cc_final: 0.8735 (tm-30)
REVERT: A  167 ASP cc_start: 0.5384 (OUTLIER) cc_final: 0.5085 (m-30)
REVERT: A  320 LEU cc_start: 0.8436 (tt) cc_final: 0.8069 (pp)
REVERT: A  339 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8078 (pt0)
REVERT: A  412 ASN cc_start: 0.7283 (m-40) cc_final: 0.6965 (m110)
REVERT: A  437 MET cc_start: 0.8229 (tpt) cc_final: 0.7973 (tpt)
REVERT: A  803 ILE cc_start: 0.6734 (OUTLIER) cc_final: 0.6378 (tp)
REVERT: A  871 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7484 (pm20)
REVERT: C   51 LEU cc_start: 0.7829 (tt) cc_final: 0.7126 (mp)
  outliers start: 45
  outliers final: 19
  residues processed: 177
  average time/residue: 0.3334
  time to fit residues: 80.2626
Evaluate side-chains
  148 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
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  264 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  637 SER
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  715 THR
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0170
   chunk 7 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 71 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 20 optimal weight:    8.9990
   overall best weight:    0.9022

-------------------------------------------------------------------------------
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
** 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 = 0.4287 r_free = 0.4287 target = 0.122756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.096514 restraints weight = 22357.879|
|-----------------------------------------------------------------------------|
r_work (start): 0.3792 rms_B_bonded: 4.38
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.3451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7777  Z= 0.138
  Angle     :  0.636   7.938  10534  Z= 0.329
  Chirality :  0.043   0.210   1243
  Planarity :  0.005   0.072   1327
  Dihedral  :  8.799 123.519   1088
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 30.49 %
    Favored  : 63.82 %
  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:  1.08 (0.23), residues: 482
  sheet: -0.72 (0.45), residues: 125
  loop : -0.58 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 766 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.013   0.002   PHE C  80 
 TYR   0.016   0.001   TYR C 143 
 ARG   0.010   0.001   ARG C  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03922 (  423)
  hydrogen bonds       : angle       4.66002 ( 1293)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       1.09299 (    2)
  covalent geometry    : bond        0.00317 ( 7776)
  covalent geometry    : angle       0.63595 (10532)

*********************** 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
  181 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 133
  time to evaluate  : 0.878 
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: 0.3270 (m-30) cc_final: 0.2831 (m-30)
REVERT: A  129 GLU cc_start: 0.8937 (tp30) cc_final: 0.8687 (tm-30)
REVERT: A  167 ASP cc_start: 0.5366 (OUTLIER) cc_final: 0.5066 (m-30)
REVERT: A  320 LEU cc_start: 0.8400 (tt) cc_final: 0.8062 (pp)
REVERT: A  339 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8043 (pt0)
REVERT: A  570 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7299 (p)
REVERT: A  677 LEU cc_start: 0.8105 (pt) cc_final: 0.7710 (pt)
REVERT: A  803 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6407 (tp)
REVERT: A  871 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7464 (pm20)
REVERT: C  115 MET cc_start: 0.8608 (mmt) cc_final: 0.7733 (tmm)
  outliers start: 48
  outliers final: 25
  residues processed: 171
  average time/residue: 0.2338
  time to fit residues: 54.7838
Evaluate side-chains
  155 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 125
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
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  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  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  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  871 GLU
Chi-restraints excluded: chain A residue  879 LEU
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:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 45 optimal weight:    7.9990
   chunk 89 optimal weight:   30.0000
   chunk 50 optimal weight:   10.0000
   chunk 88 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 14 optimal weight:    9.9990
   chunk 68 optimal weight:    0.9990
   chunk 38 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
A  43 GLN
A 140 HIS
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.116969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.091501 restraints weight = 22586.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 4.25
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.4017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064   7777  Z= 0.242
  Angle     :  0.715  14.275  10534  Z= 0.369
  Chirality :  0.046   0.334   1243
  Planarity :  0.005   0.059   1327
  Dihedral  :  8.905 131.056   1088
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 18.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 30.01 %
    Favored  : 63.23 %
  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:  0.00 (0.26), residues: 987
  helix:  0.86 (0.23), residues: 480
  sheet: -0.97 (0.42), residues: 141
  loop : -0.60 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP A 766 
 HIS   0.003   0.001   HIS A 372 
 PHE   0.040   0.003   PHE C  80 
 TYR   0.023   0.002   TYR C 143 
 ARG   0.009   0.001   ARG C  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04419 (  423)
  hydrogen bonds       : angle       4.92803 ( 1293)
  SS BOND              : bond        0.00291 (    1)
  SS BOND              : angle       1.04473 (    2)
  covalent geometry    : bond        0.00563 ( 7776)
  covalent geometry    : angle       0.71448 (10532)

*********************** 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: 57
    poor density    : 121
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 MET cc_start: 0.7597 (mpp) cc_final: 0.7236 (mpp)
REVERT: A  129 GLU cc_start: 0.8965 (tp30) cc_final: 0.8717 (tm-30)
REVERT: A  320 LEU cc_start: 0.8474 (tt) cc_final: 0.8170 (pp)
REVERT: A  339 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8049 (pt0)
REVERT: A  359 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7788 (tm-30)
REVERT: A  437 MET cc_start: 0.8412 (tpt) cc_final: 0.8033 (tpt)
REVERT: A  458 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7504 (tt0)
REVERT: A  677 LEU cc_start: 0.8170 (pt) cc_final: 0.7720 (pt)
REVERT: A  761 LYS cc_start: 0.7450 (tmtt) cc_final: 0.7208 (tmtt)
REVERT: A  779 ILE cc_start: 0.8431 (mt) cc_final: 0.8169 (mt)
REVERT: A  871 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7438 (pm20)
REVERT: C   78 ARG cc_start: 0.8236 (tpt-90) cc_final: 0.8031 (tpt90)
REVERT: C  115 MET cc_start: 0.8623 (mmt) cc_final: 0.7689 (tmm)
  outliers start: 57
  outliers final: 37
  residues processed: 168
  average time/residue: 0.1987
  time to fit residues: 46.1005
Evaluate side-chains
  151 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 111
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  788 CYS
Chi-restraints excluded: chain A residue  798 LEU
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 A residue  894 ILE
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  112 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 72 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 114 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 = 0.4239 r_free = 0.4239 target = 0.119204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.094156 restraints weight = 22506.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 4.41
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
moved from start:          0.4138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7777  Z= 0.144
  Angle     :  0.658  11.665  10534  Z= 0.333
  Chirality :  0.042   0.163   1243
  Planarity :  0.005   0.056   1327
  Dihedral  :  8.796 126.086   1088
  Min Nonbonded Distance : 2.075

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 31.32 %
    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:  0.23 (0.26), residues: 987
  helix:  1.12 (0.23), residues: 483
  sheet: -0.91 (0.42), residues: 136
  loop : -0.60 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP A 766 
 HIS   0.003   0.001   HIS C  86 
 PHE   0.037   0.002   PHE C  80 
 TYR   0.024   0.001   TYR C 143 
 ARG   0.004   0.000   ARG A 796 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03977 (  423)
  hydrogen bonds       : angle       4.68415 ( 1293)
  SS BOND              : bond        0.00032 (    1)
  SS BOND              : angle       0.56676 (    2)
  covalent geometry    : bond        0.00336 ( 7776)
  covalent geometry    : angle       0.65775 (10532)

*********************** 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
  170 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 125
  time to evaluate  : 1.812 
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: 0.8505 (mm110) cc_final: 0.8291 (tm-30)
REVERT: A   85 MET cc_start: 0.7532 (mpp) cc_final: 0.7192 (mpp)
REVERT: A  320 LEU cc_start: 0.8359 (tt) cc_final: 0.8129 (pp)
REVERT: A  339 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8104 (pt0)
REVERT: A  458 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7509 (tt0)
REVERT: A  496 LYS cc_start: 0.9456 (mmmt) cc_final: 0.9214 (tppt)
REVERT: A  538 PHE cc_start: 0.7830 (t80) cc_final: 0.7614 (t80)
REVERT: A  761 LYS cc_start: 0.7410 (tmtt) cc_final: 0.7152 (tmtt)
REVERT: A  778 LYS cc_start: 0.8178 (tppp) cc_final: 0.7869 (mtmm)
REVERT: A  779 ILE cc_start: 0.8310 (mt) cc_final: 0.8003 (mt)
REVERT: A  820 MET cc_start: 0.6342 (tmm) cc_final: 0.6141 (tmm)
REVERT: A  871 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7454 (pm20)
REVERT: C   51 LEU cc_start: 0.7373 (mp) cc_final: 0.6847 (tt)
REVERT: C  115 MET cc_start: 0.8515 (mmt) cc_final: 0.7461 (tmm)
  outliers start: 45
  outliers final: 34
  residues processed: 160
  average time/residue: 0.2502
  time to fit residues: 54.8187
Evaluate side-chains
  147 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 110
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  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  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  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  808 THR
Chi-restraints excluded: chain A residue  825 SER
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  894 ILE
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  112 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0470
   chunk 37 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    1.1684

-------------------------------------------------------------------------------
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
** C 114 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 = 0.4229 r_free = 0.4229 target = 0.118943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.094289 restraints weight = 22550.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 4.37
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.4300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7777  Z= 0.143
  Angle     :  0.650  11.876  10534  Z= 0.332
  Chirality :  0.043   0.165   1243
  Planarity :  0.005   0.054   1327
  Dihedral  :  8.719 123.882   1088
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  7.00 %
    Allowed  : 30.60 %
    Favored  : 62.40 %
  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 (0.27), residues: 987
  helix:  1.22 (0.23), residues: 484
  sheet: -0.74 (0.43), residues: 134
  loop : -0.67 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 766 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.031   0.002   PHE C  80 
 TYR   0.022   0.002   TYR C 143 
 ARG   0.005   0.000   ARG C  99 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  423)
  hydrogen bonds       : angle       4.60110 ( 1293)
  SS BOND              : bond        0.00012 (    1)
  SS BOND              : angle       0.49435 (    2)
  covalent geometry    : bond        0.00329 ( 7776)
  covalent geometry    : angle       0.65048 (10532)

*********************** 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
  177 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 118
  time to evaluate  : 0.969 
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: 0.8511 (mm110) cc_final: 0.8171 (tm-30)
REVERT: A   63 PHE cc_start: 0.6942 (OUTLIER) cc_final: 0.5523 (p90)
REVERT: A   85 MET cc_start: 0.7580 (mpp) cc_final: 0.7213 (mpp)
REVERT: A  167 ASP cc_start: 0.5834 (OUTLIER) cc_final: 0.5565 (m-30)
REVERT: A  243 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7665 (pm20)
REVERT: A  320 LEU cc_start: 0.8387 (tt) cc_final: 0.8148 (pp)
REVERT: A  339 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8122 (pt0)
REVERT: A  458 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.7443 (tt0)
REVERT: A  496 LYS cc_start: 0.9491 (mmmt) cc_final: 0.9256 (tppt)
REVERT: A  687 SER cc_start: 0.9236 (m) cc_final: 0.8986 (p)
REVERT: A  761 LYS cc_start: 0.7339 (tmtt) cc_final: 0.7093 (tmtt)
REVERT: A  778 LYS cc_start: 0.8180 (tppp) cc_final: 0.7857 (mtmm)
REVERT: A  779 ILE cc_start: 0.8356 (mt) cc_final: 0.8074 (mt)
REVERT: A  820 MET cc_start: 0.6484 (tmm) cc_final: 0.6258 (tmm)
REVERT: A  871 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7446 (pm20)
REVERT: C   51 LEU cc_start: 0.7363 (mp) cc_final: 0.6695 (tt)
REVERT: C  115 MET cc_start: 0.8540 (mmt) cc_final: 0.7460 (tmm)
  outliers start: 59
  outliers final: 40
  residues processed: 163
  average time/residue: 0.2130
  time to fit residues: 47.3388
Evaluate side-chains
  159 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 113
  time to evaluate  : 0.910 
-------------------------------------------------------------------------------
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  167 ASP
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  249 GLN
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  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  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  671 GLU
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  808 THR
Chi-restraints excluded: chain A residue  825 SER
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   84 ILE
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  112 TYR
Chi-restraints excluded: chain C residue  148 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 51 optimal weight:    0.4980
   chunk 24 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 70 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.4241 r_free = 0.4241 target = 0.119552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.094912 restraints weight = 22623.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 4.31
r_work: 0.3580 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.4377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7777  Z= 0.137
  Angle     :  0.661  11.464  10534  Z= 0.336
  Chirality :  0.043   0.148   1243
  Planarity :  0.005   0.054   1327
  Dihedral  :  8.661 121.377   1088
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 31.79 %
    Favored  : 62.04 %
  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:  0.37 (0.27), residues: 987
  helix:  1.28 (0.23), residues: 483
  sheet: -0.73 (0.43), residues: 135
  loop : -0.67 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.003   TRP A 766 
 HIS   0.003   0.001   HIS C  86 
 PHE   0.027   0.002   PHE C  80 
 TYR   0.022   0.002   TYR C 143 
 ARG   0.004   0.000   ARG A 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03813 (  423)
  hydrogen bonds       : angle       4.56906 ( 1293)
  SS BOND              : bond        0.00228 (    1)
  SS BOND              : angle       0.93121 (    2)
  covalent geometry    : bond        0.00322 ( 7776)
  covalent geometry    : angle       0.66109 (10532)

*********************** 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
  171 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 119
  time to evaluate  : 0.816 
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: 0.8646 (mm110) cc_final: 0.8186 (tm-30)
REVERT: A   63 PHE cc_start: 0.7231 (OUTLIER) cc_final: 0.5717 (p90)
REVERT: A   85 MET cc_start: 0.8051 (mpp) cc_final: 0.7560 (mpp)
REVERT: A  167 ASP cc_start: 0.5930 (OUTLIER) cc_final: 0.5696 (m-30)
REVERT: A  243 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7583 (pm20)
REVERT: A  320 LEU cc_start: 0.8600 (tt) cc_final: 0.8297 (pp)
REVERT: A  339 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8210 (pt0)
REVERT: A  458 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7495 (tt0)
REVERT: A  496 LYS cc_start: 0.9463 (mmmt) cc_final: 0.9240 (tppt)
REVERT: A  570 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7465 (p)
REVERT: A  687 SER cc_start: 0.9198 (m) cc_final: 0.8949 (p)
REVERT: A  761 LYS cc_start: 0.7394 (tmtt) cc_final: 0.7004 (tmtt)
REVERT: A  778 LYS cc_start: 0.8453 (tppp) cc_final: 0.7884 (mtmm)
REVERT: A  779 ILE cc_start: 0.8396 (mt) cc_final: 0.8098 (mt)
REVERT: A  820 MET cc_start: 0.6814 (tmm) cc_final: 0.6596 (tmm)
REVERT: A  871 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7530 (pm20)
REVERT: C   51 LEU cc_start: 0.7939 (mp) cc_final: 0.7390 (tt)
REVERT: C  112 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.8904 (m-80)
REVERT: C  115 MET cc_start: 0.8690 (mmt) cc_final: 0.7511 (tmm)
  outliers start: 52
  outliers final: 36
  residues processed: 159
  average time/residue: 0.1981
  time to fit residues: 42.6719
Evaluate side-chains
  159 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 115
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
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  188 LEU
Chi-restraints excluded: chain A residue  243 GLU
Chi-restraints excluded: chain A residue  247 MET
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  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  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  594 VAL
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  621 SER
Chi-restraints excluded: chain A residue  637 SER
Chi-restraints excluded: chain A residue  715 THR
Chi-restraints excluded: chain A residue  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  808 THR
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  112 TYR
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:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 43 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 69 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 41 optimal weight:    9.9990
   chunk 95 optimal weight:    5.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4258 r_free = 0.4258 target = 0.120345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.094954 restraints weight = 22706.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 4.34
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.4508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7777  Z= 0.136
  Angle     :  0.669  11.346  10534  Z= 0.340
  Chirality :  0.042   0.155   1243
  Planarity :  0.004   0.054   1327
  Dihedral  :  8.609 119.222   1088
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 32.03 %
    Favored  : 61.80 %
  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:  0.43 (0.27), residues: 987
  helix:  1.32 (0.23), residues: 482
  sheet: -0.61 (0.44), residues: 131
  loop : -0.67 (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   0.038   0.002   PHE C  80 
 TYR   0.021   0.002   TYR C 143 
 ARG   0.005   0.000   ARG C  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03796 (  423)
  hydrogen bonds       : angle       4.50053 ( 1293)
  SS BOND              : bond        0.00155 (    1)
  SS BOND              : angle       0.62464 (    2)
  covalent geometry    : bond        0.00320 ( 7776)
  covalent geometry    : angle       0.66877 (10532)

*********************** 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
  167 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 115
  time to evaluate  : 0.840 
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: 0.8584 (mm110) cc_final: 0.8168 (tm-30)
REVERT: A   63 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.5491 (p90)
REVERT: A   84 ILE cc_start: 0.7961 (mm) cc_final: 0.7754 (mm)
REVERT: A   85 MET cc_start: 0.7588 (mpp) cc_final: 0.7183 (mpp)
REVERT: A  167 ASP cc_start: 0.5756 (OUTLIER) cc_final: 0.5485 (m-30)
REVERT: A  243 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7738 (pm20)
REVERT: A  320 LEU cc_start: 0.8374 (tt) cc_final: 0.8146 (pp)
REVERT: A  339 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8060 (pt0)
REVERT: A  417 ARG cc_start: 0.8802 (ttt-90) cc_final: 0.8387 (ttp80)
REVERT: A  458 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7496 (tt0)
REVERT: A  496 LYS cc_start: 0.9452 (mmmt) cc_final: 0.9219 (tppt)
REVERT: A  570 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7346 (p)
REVERT: A  687 SER cc_start: 0.9229 (m) cc_final: 0.8986 (p)
REVERT: A  761 LYS cc_start: 0.7411 (tmtt) cc_final: 0.7074 (tmtt)
REVERT: A  778 LYS cc_start: 0.8198 (tppp) cc_final: 0.7856 (mtmm)
REVERT: A  779 ILE cc_start: 0.8369 (mt) cc_final: 0.8079 (mt)
REVERT: A  820 MET cc_start: 0.6440 (tmm) cc_final: 0.6196 (tmm)
REVERT: A  871 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7416 (pm20)
REVERT: C   51 LEU cc_start: 0.7667 (mp) cc_final: 0.7134 (tt)
REVERT: C  115 MET cc_start: 0.8670 (mmt) cc_final: 0.7412 (tmm)
  outliers start: 52
  outliers final: 39
  residues processed: 155
  average time/residue: 0.1975
  time to fit residues: 41.4022
Evaluate side-chains
  157 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 111
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
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  167 ASP
Chi-restraints excluded: chain A residue  175 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  442 LEU
Chi-restraints excluded: chain A residue  458 GLN
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  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  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  783 SER
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  825 SER
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain 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:    3.9990
   chunk 78 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 62 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 3 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    1.8986

-------------------------------------------------------------------------------
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**
** A 364 HIS ** 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 = 0.4203 r_free = 0.4203 target = 0.117531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.092448 restraints weight = 22559.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3712 rms_B_bonded: 4.19
r_work: 0.3548 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.4683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   7777  Z= 0.177
  Angle     :  0.700  12.865  10534  Z= 0.354
  Chirality :  0.043   0.168   1243
  Planarity :  0.005   0.055   1327
  Dihedral  :  8.667 121.194   1088
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 32.38 %
    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:  0.37 (0.27), residues: 987
  helix:  1.22 (0.23), residues: 482
  sheet: -0.54 (0.44), residues: 129
  loop : -0.65 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP A 766 
 HIS   0.003   0.001   HIS A 140 
 PHE   0.038   0.002   PHE C  80 
 TYR   0.022   0.002   TYR C 143 
 ARG   0.011   0.001   ARG A 760 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03967 (  423)
  hydrogen bonds       : angle       4.58561 ( 1293)
  SS BOND              : bond        0.00088 (    1)
  SS BOND              : angle       0.82902 (    2)
  covalent geometry    : bond        0.00417 ( 7776)
  covalent geometry    : angle       0.70001 (10532)

********************** 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
  159 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 111
  time to evaluate  : 0.813 
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: 0.8755 (mm110) cc_final: 0.8318 (tm-30)
REVERT: A   63 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.5485 (p90)
REVERT: A   85 MET cc_start: 0.8036 (mpp) cc_final: 0.7569 (mpp)
REVERT: A  320 LEU cc_start: 0.8635 (tt) cc_final: 0.8300 (pp)
REVERT: A  339 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8146 (pt0)
REVERT: A  458 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7518 (tt0)
REVERT: A  496 LYS cc_start: 0.9515 (mmmt) cc_final: 0.9290 (tppt)
REVERT: A  687 SER cc_start: 0.9215 (m) cc_final: 0.8986 (p)
REVERT: A  779 ILE cc_start: 0.8457 (mt) cc_final: 0.8237 (mt)
REVERT: A  820 MET cc_start: 0.6758 (tmm) cc_final: 0.6540 (tmm)
REVERT: A  871 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7559 (pm20)
REVERT: C   51 LEU cc_start: 0.8047 (mp) cc_final: 0.7512 (tt)
REVERT: C  115 MET cc_start: 0.8771 (mmt) cc_final: 0.7297 (tmm)
  outliers start: 48
  outliers final: 41
  residues processed: 151
  average time/residue: 0.1831
  time to fit residues: 38.1812
Evaluate side-chains
  152 residues out of total 847 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 107
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
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  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  339 GLU
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  410 VAL
Chi-restraints excluded: chain A residue  426 THR
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  458 GLN
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  527 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  637 SER
Chi-restraints excluded: chain A residue  686 MET
Chi-restraints excluded: chain A residue  695 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  783 SER
Chi-restraints excluded: chain A residue  788 CYS
Chi-restraints excluded: chain A residue  798 LEU
Chi-restraints excluded: chain A residue  808 THR
Chi-restraints excluded: chain A residue  825 SER
Chi-restraints excluded: chain A residue  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:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 57 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 61 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   chunk 96 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.119754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.094648 restraints weight = 22429.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 4.33
r_work: 0.3592 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.4751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7777  Z= 0.133
  Angle     :  0.685  11.650  10534  Z= 0.346
  Chirality :  0.043   0.196   1243
  Planarity :  0.004   0.054   1327
  Dihedral  :  8.533 117.403   1088
  Min Nonbonded Distance : 2.085

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 32.74 %
    Favored  : 62.04 %
  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:  0.44 (0.27), residues: 987
  helix:  1.31 (0.23), residues: 478
  sheet: -0.55 (0.44), residues: 129
  loop : -0.63 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 766 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.034   0.001   PHE C  80 
 TYR   0.021   0.002   TYR C 143 
 ARG   0.004   0.000   ARG A 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03792 (  423)
  hydrogen bonds       : angle       4.49752 ( 1293)
  SS BOND              : bond        0.00065 (    1)
  SS BOND              : angle       0.68166 (    2)
  covalent geometry    : bond        0.00311 ( 7776)
  covalent geometry    : angle       0.68505 (10532)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4190.76 seconds
wall clock time: 75 minutes 17.87 seconds (4517.87 seconds total)