Starting phenix.real_space_refine
on Sat Oct 11 02:05:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8omq_16974/10_2025/8omq_16974.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8omq_16974/10_2025/8omq_16974.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8omq_16974/10_2025/8omq_16974.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8omq_16974/10_2025/8omq_16974.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8omq_16974/10_2025/8omq_16974.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8omq_16974/10_2025/8omq_16974.map"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
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
     P       6      5.49       5
     Mg      2      5.21       5
     S      54      5.16       5
     C    6707      2.51       5
     N    1811      2.21       5
     O    2004      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10584
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 4634
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 577, 4631
          Classifications: {'peptide': 577}
          Link IDs: {'PTRANS': 17, 'TRANS': 559}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 577, 4631
          Classifications: {'peptide': 577}
          Link IDs: {'PTRANS': 17, 'TRANS': 559}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4716
    Chain: "A"
      Number of atoms: 5886
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 745, 5883
          Classifications: {'peptide': 745}
          Link IDs: {'PTRANS': 22, 'TRANS': 722}
          Chain breaks: 6
      Conformer: "B"
        Number of residues, atoms: 745, 5883
          Classifications: {'peptide': 745}
          Link IDs: {'PTRANS': 22, 'TRANS': 722}
          Chain breaks: 6
          bond proxies already assigned to first conformer: 5960
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 4.81, per 1000 atoms: 0.45
  Number of scatterers: 10584
  At special positions: 0
  Unit cell: (85.0206, 108.79, 171.87, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      54     16.00
     P       6     15.00
     Mg      2     11.99
     O    2004      8.00
     N    1811      7.00
     C    6707      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.94
  Conformation dependent library (CDL) restraints added in 913.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2514

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 7 sheets defined
      58.9% alpha, 8.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'B' and resid 538 through 545
    Processing helix  chain 'B' and resid 559 through 565
    Processing helix  chain 'B' and resid 569 through 582
      removed outlier: 3.641A  pdb=" N   ARG B 573 " --> pdb=" O   THR B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 603
      removed outlier: 3.604A  pdb=" N   ILE B 590 " --> pdb=" O   LYS B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 606 through 617
      removed outlier: 4.709A  pdb=" N   LYS B 617 " --> pdb=" O   ASN B 613 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 620 through 630
    Processing helix  chain 'B' and resid 634 through 654
    Processing helix  chain 'B' and resid 655 through 663
    Processing helix  chain 'B' and resid 665 through 673
    Processing helix  chain 'B' and resid 674 through 679
      removed outlier: 3.510A  pdb=" N   LEU B 678 " --> pdb=" O   GLU B 674 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 680 through 682
      No H-bonds generated for 'chain 'B' and resid 680 through 682'
    Processing helix  chain 'B' and resid 683 through 688
    Processing helix  chain 'B' and resid 690 through 697
      removed outlier: 3.941A  pdb=" N   VAL B 696 " --> pdb=" O   GLN B 692 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   GLY B 697 " --> pdb=" O   ALA B 693 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 708
    Processing helix  chain 'B' and resid 709 through 729
      removed outlier: 3.965A  pdb=" N   LYS B 713 " --> pdb=" O   PHE B 709 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   HIS B 729 " --> pdb=" O   GLU B 725 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 729 through 738
    Processing helix  chain 'B' and resid 782 through 815
    Processing helix  chain 'B' and resid 817 through 843
    Processing helix  chain 'B' and resid 864 through 871
    Processing helix  chain 'B' and resid 901 through 919
    Processing helix  chain 'B' and resid 944 through 948
      removed outlier: 3.844A  pdb=" N   GLY B 948 " --> pdb=" O   ILE B 945 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 950 through 965
    Processing helix  chain 'B' and resid 982 through 1000
    Processing helix  chain 'B' and resid 1011 through 1016
    Processing helix  chain 'B' and resid 1017 through 1021
    Processing helix  chain 'B' and resid 1068 through 1076
      removed outlier: 3.681A  pdb=" N   VAL B1072 " --> pdb=" O   TYR B1068 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1079 through 1111
    Processing helix  chain 'B' and resid 1115 through 1121
      removed outlier: 3.539A  pdb=" N   LYS B1121 " --> pdb=" O   GLN B1117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 195
    Processing helix  chain 'A' and resid 210 through 219
    Processing helix  chain 'A' and resid 228 through 232
    Processing helix  chain 'A' and resid 236 through 244
      removed outlier: 3.686A  pdb=" N   ARG A 243 " --> pdb=" O   GLN A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 262
      removed outlier: 3.568A  pdb=" N   GLU A 262 " --> pdb=" O   PRO A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 275
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 303 through 311
    Processing helix  chain 'A' and resid 326 through 331
    Processing helix  chain 'A' and resid 335 through 348
      removed outlier: 3.603A  pdb=" N   ARG A 340 " --> pdb=" O   PRO A 336 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LEU A 341 " --> pdb=" O   GLN A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 369
      removed outlier: 3.574A  pdb=" N   ILE A 356 " --> pdb=" O   ASP A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 378
    Processing helix  chain 'A' and resid 380 through 384
    Processing helix  chain 'A' and resid 388 through 396
    Processing helix  chain 'A' and resid 400 through 413
      removed outlier: 3.540A  pdb=" N   GLN A 413 " --> pdb=" O   GLN A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 424
    Processing helix  chain 'A' and resid 429 through 456
      Proline residue:  A 439  - end of helix
      removed outlier: 4.666A  pdb=" N   LYS A 449 " --> pdb=" O   SER A 445 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   PHE A 450 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   MET A 453 " --> pdb=" O   LYS A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 504
      removed outlier: 3.551A  pdb=" N   ARG A 482 " --> pdb=" O   LEU A 478 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   GLU A 483 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   ILE A 484 " --> pdb=" O   GLU A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 532
      removed outlier: 3.927A  pdb=" N   GLU A 530 " --> pdb=" O   CYS A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 586
      removed outlier: 3.653A  pdb=" N   ILE A 577 " --> pdb=" O   ALA A 573 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS A 579 " --> pdb=" O   ASP A 575 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   GLU A 580 " --> pdb=" O   ALA A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 613
      removed outlier: 3.873A  pdb=" N   VAL A 598 " --> pdb=" O   THR A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 645
      removed outlier: 3.598A  pdb=" N   VAL A 644 " --> pdb=" O   CYS A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 692
      removed outlier: 3.852A  pdb=" N   GLY A 683 " --> pdb=" O   ILE A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 736
    Processing helix  chain 'A' and resid 755 through 774
      removed outlier: 3.535A  pdb=" N   ILE A 774 " --> pdb=" O   ILE A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 784 through 788
      removed outlier: 3.779A  pdb=" N   THR A 788 " --> pdb=" O   HIS A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 794
      removed outlier: 3.663A  pdb=" N   GLN A 793 " --> pdb=" O   ALA A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 834
      removed outlier: 3.702A  pdb=" N   VAL A 830 " --> pdb=" O   PHE A 826 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 837 through 850
    Processing helix  chain 'A' and resid 871 through 893
      removed outlier: 3.769A  pdb=" N   ILE A 884 " --> pdb=" O   GLY A 880 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLN A 885 " --> pdb=" O   GLU A 881 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 919
      removed outlier: 3.720A  pdb=" N   ILE A 904 " --> pdb=" O   SER A 900 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   THR A 905 " --> pdb=" O   GLU A 901 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   GLU A 914 " --> pdb=" O   GLN A 910 " (cutoff:3.500A)
      removed outlier: 4.158A  pdb=" N   VAL A 915 " --> pdb=" O   LEU A 911 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   ILE A 916 " --> pdb=" O   LYS A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 930
    Processing sheet with id=AA1, first strand: chain 'B' and resid 754 through 757
    Processing sheet with id=AA2, first strand: chain 'B' and resid 880 through 884
      removed outlier: 5.042A  pdb=" N   ASN B 880 " --> pdb=" O   ASN B 861 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASN B 861 " --> pdb=" O   ASN B 880 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLU B 926 " --> pdb=" O   LYS B 860 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 935 through 938
      removed outlier: 6.383A  pdb=" N   PHE B 936 " --> pdb=" O   ILE B 973 " (cutoff:3.500A)
      removed outlier: 7.785A  pdb=" N   ASP B 975 " --> pdb=" O   PHE B 936 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ARG B 938 " --> pdb=" O   ASP B 975 " (cutoff:3.500A)
      removed outlier: 7.104A  pdb=" N   TYR B1028 " --> pdb=" O   VAL B 891 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   ILE B 893 " --> pdb=" O   TYR B1028 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   MET B1030 " --> pdb=" O   ILE B 893 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   THR B 895 " --> pdb=" O   MET B1030 " (cutoff:3.500A)
      removed outlier: 8.604A  pdb=" N   PHE B1032 " --> pdb=" O   THR B 895 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   ASN B1027 " --> pdb=" O   THR B1060 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   THR B1060 " --> pdb=" O   ASN B1027 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   HIS B1029 " --> pdb=" O   GLN B1058 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   GLN B1058 " --> pdb=" O   HIS B1029 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLY B1031 " --> pdb=" O   LEU B1056 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU B1056 " --> pdb=" O   GLY B1031 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 147 through 153
      removed outlier: 6.308A  pdb=" N   LEU A 173 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 302
      removed outlier: 6.822A  pdb=" N   LYS A 301 " --> pdb=" O   ILE A 708 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   ALA A 710 " --> pdb=" O   LYS A 301 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   CYS A 707 " --> pdb=" O   LEU A 744 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   ILE A 746 " --> pdb=" O   CYS A 707 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   LEU A 709 " --> pdb=" O   ILE A 746 " (cutoff:3.500A)
      removed outlier: 5.614A  pdb=" N   SER A 743 " --> pdb=" O   PHE A 777 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   MET A 779 " --> pdb=" O   SER A 743 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   ILE A 745 " --> pdb=" O   MET A 779 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ALA A 781 " --> pdb=" O   ILE A 745 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   ILE A 747 " --> pdb=" O   ALA A 781 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   ASN A 799 " --> pdb=" O   LYS A 818 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LYS A 818 " --> pdb=" O   ASN A 799 " (cutoff:3.500A)
      removed outlier: 5.951A  pdb=" N   HIS A 801 " --> pdb=" O   GLN A 816 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   GLN A 816 " --> pdb=" O   HIS A 801 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   THR A 803 " --> pdb=" O   LEU A 814 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A 814 " --> pdb=" O   THR A 803 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 540 through 543
      removed outlier: 4.538A  pdb=" N   VAL A 542 " --> pdb=" O   LYS A 550 " (cutoff:3.500A)
      removed outlier: 8.015A  pdb=" N   LYS A 550 " --> pdb=" O   VAL A 542 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 653 through 657
      removed outlier: 5.059A  pdb=" N   ASN A 653 " --> pdb=" O   ALA A 636 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ALA A 636 " --> pdb=" O   ASN A 653 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   SER A 699 " --> pdb=" O   LYS A 635 " (cutoff:3.500A)

    553 hydrogen bonds defined for protein.
    1589 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.97

  Time building geometry restraints manager: 1.28 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2908
        1.34 -     1.46: 2840
        1.46 -     1.58: 4915
        1.58 -     1.70: 9
        1.70 -     1.82: 86
  Bond restraints: 10758
  Sorted by residual:
  bond pdb=" CA  SER B 904 "
       pdb=" CB  SER B 904 "
    ideal  model  delta    sigma   weight residual
    1.528  1.491  0.038 1.56e-02 4.11e+03 5.89e+00
  bond pdb=" CA  SER A 607 "
       pdb=" CB  SER A 607 "
    ideal  model  delta    sigma   weight residual
    1.529  1.491  0.038 1.58e-02 4.01e+03 5.89e+00
  bond pdb=" CA  SER A 825 "
       pdb=" CB  SER A 825 "
    ideal  model  delta    sigma   weight residual
    1.530  1.489  0.041 1.68e-02 3.54e+03 5.85e+00
  bond pdb=" CA  SER B 559 "
       pdb=" CB  SER B 559 "
    ideal  model  delta    sigma   weight residual
    1.535  1.495  0.040 1.71e-02 3.42e+03 5.58e+00
  bond pdb=" CE1 HIS A 665 "
       pdb=" NE2 HIS A 665 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.27e+00
  ... (remaining 10753 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.14: 14458
        4.14 -     8.28: 60
        8.28 -    12.42: 2
       12.42 -    16.56: 1
       16.56 -    20.70: 3
  Bond angle restraints: 14524
  Sorted by residual:
  angle pdb=" PA  ATP A2000 "
        pdb=" O3A ATP A2000 "
        pdb=" PB  ATP A2000 "
      ideal   model   delta    sigma   weight residual
     136.83  116.13   20.70 1.00e+00 1.00e+00 4.29e+02
  angle pdb=" PA  ATP B2000 "
        pdb=" O3A ATP B2000 "
        pdb=" PB  ATP B2000 "
      ideal   model   delta    sigma   weight residual
     136.83  117.40   19.43 1.00e+00 1.00e+00 3.77e+02
  angle pdb=" PB  ATP A2000 "
        pdb=" O3B ATP A2000 "
        pdb=" PG  ATP A2000 "
      ideal   model   delta    sigma   weight residual
     139.87  122.47   17.40 1.00e+00 1.00e+00 3.03e+02
  angle pdb=" PB  ATP B2000 "
        pdb=" O3B ATP B2000 "
        pdb=" PG  ATP B2000 "
      ideal   model   delta    sigma   weight residual
     139.87  123.91   15.96 1.00e+00 1.00e+00 2.55e+02
  angle pdb=" C5' ATP B2000 "
        pdb=" O5' ATP B2000 "
        pdb=" PA  ATP B2000 "
      ideal   model   delta    sigma   weight residual
     121.27  110.88   10.39 1.00e+00 1.00e+00 1.08e+02
  ... (remaining 14519 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 5740
       17.34 -    34.68: 645
       34.68 -    52.02: 177
       52.02 -    69.36: 47
       69.36 -    86.70: 20
  Dihedral angle restraints: 6629
    sinusoidal: 2763
      harmonic: 3866
  Sorted by residual:
  dihedral pdb=" CA  THR A 438 "
           pdb=" C   THR A 438 "
           pdb=" N   PRO A 439 "
           pdb=" CA  PRO A 439 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.65   24.35     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  GLY B 900 "
           pdb=" C   GLY B 900 "
           pdb=" N   GLY B 901 "
           pdb=" CA  GLY B 901 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.06  -22.94     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" C   LYS B 738 "
           pdb=" N   LYS B 738 "
           pdb=" CA  LYS B 738 "
           pdb=" CB  LYS B 738 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.89    9.29     0      2.50e+00 1.60e-01 1.38e+01
  ... (remaining 6626 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 872
       0.064 -    0.129: 599
       0.129 -    0.193: 172
       0.193 -    0.258: 26
       0.258 -    0.322: 2
  Chirality restraints: 1671
  Sorted by residual:
  chirality pdb=" CA  LYS B 738 "
            pdb=" N   LYS B 738 "
            pdb=" C   LYS B 738 "
            pdb=" CB  LYS B 738 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" CA  THR A 438 "
            pdb=" N   THR A 438 "
            pdb=" C   THR A 438 "
            pdb=" CB  THR A 438 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.24    0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" CA  GLU A 878 "
            pdb=" N   GLU A 878 "
            pdb=" C   GLU A 878 "
            pdb=" CB  GLU A 878 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1668 not shown)

  Planarity restraints: 1844
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' ATP A2000 "   -0.026 2.00e-02 2.50e+03   1.36e-02 5.06e+00
        pdb=" C2  ATP A2000 "    0.013 2.00e-02 2.50e+03
        pdb=" C4  ATP A2000 "    0.002 2.00e-02 2.50e+03
        pdb=" C5  ATP A2000 "    0.004 2.00e-02 2.50e+03
        pdb=" C6  ATP A2000 "    0.008 2.00e-02 2.50e+03
        pdb=" C8  ATP A2000 "    0.017 2.00e-02 2.50e+03
        pdb=" N1  ATP A2000 "    0.002 2.00e-02 2.50e+03
        pdb=" N3  ATP A2000 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6  ATP A2000 "   -0.027 2.00e-02 2.50e+03
        pdb=" N7  ATP A2000 "    0.006 2.00e-02 2.50e+03
        pdb=" N9  ATP A2000 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 438 "    0.008 2.00e-02 2.50e+03   1.52e-02 2.32e+00
        pdb=" C   THR A 438 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   THR A 438 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PRO A 439 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 579 "   -0.017 2.00e-02 2.50e+03   8.69e-03 1.89e+00
        pdb=" CG  TRP B 579 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 579 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 579 "    0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 579 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 579 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 579 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 579 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 579 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 579 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1841 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.46: 48
        2.46 -     3.07: 7271
        3.07 -     3.68: 17292
        3.68 -     4.29: 25097
        4.29 -     4.90: 40668
  Nonbonded interactions: 90376
  Sorted by model distance:
  nonbonded pdb=" O2G ATP B2000 "
            pdb="MG    MG B2001 "
     model   vdw
     1.847 2.170
  nonbonded pdb=" OG  SER A 676 "
            pdb="MG    MG A2001 "
     model   vdw
     1.944 2.170
  nonbonded pdb=" O2B ATP A2000 "
            pdb="MG    MG A2001 "
     model   vdw
     1.946 2.170
  nonbonded pdb=" OG  SER B 903 "
            pdb="MG    MG B2001 "
     model   vdw
     2.087 2.170
  nonbonded pdb=" O2G ATP A2000 "
            pdb="MG    MG A2001 "
     model   vdw
     2.109 2.170
  ... (remaining 90371 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=0.50 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:             3.200
  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:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.810
  Find NCS groups from input model:        0.060
  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:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
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      :  0.007   0.048  10758  Z= 0.452
  Angle     :  1.226  20.705  14524  Z= 0.856
  Chirality :  0.084   0.322   1671
  Planarity :  0.004   0.034   1844
  Dihedral  : 16.896  86.699   4115
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 16.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 13.48 %
    Favored  : 83.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.30 (0.20), residues: 1306
  helix: -1.56 (0.17), residues: 704
  sheet: -3.24 (0.39), residues: 120
  loop : -2.66 (0.26), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 680 
 TYR   0.018   0.003   TYR A 405 
 PHE   0.014   0.003   PHE A 836 
 TRP   0.017   0.004   TRP B 579 
 HIS   0.013   0.002   HIS A 610 

Details of bonding type rmsd
  covalent geometry    : bond        0.00673 (10758)
  covalent geometry    : angle       1.22638 (14524)
  hydrogen bonds       : bond        0.14411 (  553)
  hydrogen bonds       : angle       6.39527 ( 1589)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 315
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  532 MET cc_start: 0.7284 (ttt) cc_final: 0.6885 (ttt)
REVERT: B  534 PHE cc_start: 0.8237 (m-80) cc_final: 0.7665 (m-80)
REVERT: B  554 MET cc_start: 0.8315 (mmt) cc_final: 0.7982 (mmm)
REVERT: B  573 ARG cc_start: 0.7730 (ttt-90) cc_final: 0.7513 (ttt-90)
REVERT: B  785 ILE cc_start: 0.7398 (mt) cc_final: 0.7172 (mt)
REVERT: B  809 ASP cc_start: 0.7531 (t0) cc_final: 0.7185 (t0)
REVERT: B  852 GLN cc_start: 0.8695 (mt0) cc_final: 0.8404 (mt0)
REVERT: B  856 LYS cc_start: 0.8500 (tttt) cc_final: 0.8168 (tttp)
REVERT: B  863 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7499 (ptp-110)
REVERT: B  953 MET cc_start: 0.7906 (tpt) cc_final: 0.7360 (tpt)
REVERT: B 1077 ASP cc_start: 0.7865 (t0) cc_final: 0.7524 (t0)
REVERT: B 1084 LYS cc_start: 0.8295 (tptp) cc_final: 0.7989 (tptp)
REVERT: A  172 LYS cc_start: 0.7389 (tttp) cc_final: 0.6874 (mmmt)
REVERT: A  188 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7181 (tm-30)
REVERT: A  244 LEU cc_start: 0.7483 (tp) cc_final: 0.6730 (tp)
REVERT: A  253 MET cc_start: 0.7023 (tpt) cc_final: 0.6002 (tpt)
REVERT: A  350 LEU cc_start: 0.8175 (mt) cc_final: 0.7969 (mt)
REVERT: A  351 MET cc_start: 0.8008 (mmm) cc_final: 0.7693 (tpp)
REVERT: A  358 GLU cc_start: 0.8077 (tt0) cc_final: 0.7480 (pt0)
REVERT: A  419 GLN cc_start: 0.8458 (tt0) cc_final: 0.8223 (tt0)
REVERT: A  422 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7904 (mt-10)
REVERT: A  605 VAL cc_start: 0.8207 (t) cc_final: 0.7938 (m)
REVERT: A  619 TYR cc_start: 0.8686 (m-10) cc_final: 0.8471 (m-10)
REVERT: A  620 VAL cc_start: 0.8699 (t) cc_final: 0.8457 (m)
REVERT: A  635 LYS cc_start: 0.8464 (mptt) cc_final: 0.8262 (mptt)
REVERT: A  638 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7606 (mtm-85)
REVERT: A  720 LYS cc_start: 0.8235 (mttt) cc_final: 0.7986 (mttm)
REVERT: A  726 MET cc_start: 0.8256 (tpp) cc_final: 0.7904 (tpp)
REVERT: A  793 GLN cc_start: 0.8215 (mt0) cc_final: 0.7967 (mp10)
REVERT: A  845 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8228 (mtmm)
  outliers start: 35
  outliers final: 22
  residues processed: 341
  average time/residue: 0.1370
  time to fit residues: 62.1810
Evaluate side-chains
  300 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 278
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  744 TYR
Chi-restraints excluded: chain B residue  777 VAL
Chi-restraints excluded: chain B residue  781 HIS
Chi-restraints excluded: chain B residue  799 LEU
Chi-restraints excluded: chain B residue  817 HIS
Chi-restraints excluded: chain B residue  939 MET
Chi-restraints excluded: chain B residue 1025 VAL
Chi-restraints excluded: chain B residue 1060 THR
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  270 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  296 PHE
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  677 THR
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    0.3980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.4980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.4980
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 538 ASN
B 549 GLN
B 582 GLN
B 613 ASN
B 684 HIS
** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1098 ASN
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 GLN
A 311 ASN
A 343 ASN
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 GLN
** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 462 GLN
** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 538 ASN
A 596 ASN
A 639 HIS
A 681 GLN
A 690 GLN
A 718 GLN
A 793 GLN
** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 879 GLN
A 924 ASN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.179634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.145373 restraints weight = 34130.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3878 rms_B_bonded: 3.89
r_work: 0.3660 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3665
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3665 r_free = 0.3665    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3664 r_free = 0.3664    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3664
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10758  Z= 0.182
  Angle     :  0.667   9.294  14524  Z= 0.349
  Chirality :  0.044   0.260   1671
  Planarity :  0.004   0.038   1844
  Dihedral  :  9.609  88.498   1511
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 20.39 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.81 (0.22), residues: 1306
  helix: -0.24 (0.19), residues: 716
  sheet: -2.76 (0.41), residues: 120
  loop : -2.16 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 406 
 TYR   0.027   0.002   TYR A 815 
 PHE   0.031   0.002   PHE A 286 
 TRP   0.012   0.002   TRP B 562 
 HIS   0.015   0.002   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (10758)
  covalent geometry    : angle       0.66669 (14524)
  hydrogen bonds       : bond        0.04681 (  553)
  hydrogen bonds       : angle       4.93366 ( 1589)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 285
  time to evaluate  : 0.412 
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: B  534 PHE cc_start: 0.8220 (m-80) cc_final: 0.7660 (m-80)
REVERT: B  554 MET cc_start: 0.8198 (mmt) cc_final: 0.7960 (mmm)
REVERT: B  565 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6965 (t0)
REVERT: B  779 ARG cc_start: 0.6218 (mtm-85) cc_final: 0.5829 (mtm180)
REVERT: B  809 ASP cc_start: 0.7323 (t0) cc_final: 0.7036 (t0)
REVERT: B  852 GLN cc_start: 0.8450 (mt0) cc_final: 0.8213 (mt0)
REVERT: B  858 VAL cc_start: 0.8637 (t) cc_final: 0.8364 (m)
REVERT: B  949 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.7139 (mtm110)
REVERT: B  953 MET cc_start: 0.8051 (tpt) cc_final: 0.7798 (tpt)
REVERT: B  975 ASP cc_start: 0.8261 (t0) cc_final: 0.6946 (m-30)
REVERT: B  999 ARG cc_start: 0.8109 (ttp-170) cc_final: 0.7895 (ttp-170)
REVERT: B 1077 ASP cc_start: 0.7769 (t0) cc_final: 0.7359 (t0)
REVERT: B 1084 LYS cc_start: 0.8011 (tptp) cc_final: 0.7595 (tptp)
REVERT: B 1103 ARG cc_start: 0.7650 (mtt180) cc_final: 0.6988 (mtt-85)
REVERT: A  172 LYS cc_start: 0.7446 (tttp) cc_final: 0.7131 (mmmt)
REVERT: A  188 GLU cc_start: 0.6505 (tm-30) cc_final: 0.6261 (tm-30)
REVERT: A  244 LEU cc_start: 0.7191 (tp) cc_final: 0.6815 (tp)
REVERT: A  253 MET cc_start: 0.6734 (tpt) cc_final: 0.5606 (tpt)
REVERT: A  351 MET cc_start: 0.7686 (mmm) cc_final: 0.7309 (mmm)
REVERT: A  358 GLU cc_start: 0.7939 (tt0) cc_final: 0.7414 (pt0)
REVERT: A  359 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7827 (mtt180)
REVERT: A  369 ASP cc_start: 0.7613 (m-30) cc_final: 0.7398 (m-30)
REVERT: A  414 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7950 (mp)
REVERT: A  442 ASP cc_start: 0.8008 (t70) cc_final: 0.7747 (t0)
REVERT: A  620 VAL cc_start: 0.8635 (t) cc_final: 0.8395 (m)
REVERT: A  666 ILE cc_start: 0.8220 (mt) cc_final: 0.7114 (tp)
REVERT: A  720 LYS cc_start: 0.7660 (mttt) cc_final: 0.7453 (mttm)
REVERT: A  726 MET cc_start: 0.8177 (tpp) cc_final: 0.7792 (tpp)
REVERT: A  819 LYS cc_start: 0.8153 (tttm) cc_final: 0.7899 (tptt)
REVERT: A  845 LYS cc_start: 0.8095 (mtpt) cc_final: 0.7791 (mtmm)
  outliers start: 40
  outliers final: 26
  residues processed: 310
  average time/residue: 0.1294
  time to fit residues: 53.6420
Evaluate side-chains
  297 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 269
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  565 ASP
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  642 VAL
Chi-restraints excluded: chain B residue  644 THR
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  744 TYR
Chi-restraints excluded: chain B residue  781 HIS
Chi-restraints excluded: chain B residue  799 LEU
Chi-restraints excluded: chain B residue  882 THR
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue 1000 ASP
Chi-restraints excluded: chain B residue 1025 VAL
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  677 THR
Chi-restraints excluded: chain A residue  690 GLN
Chi-restraints excluded: chain A residue  732 THR
Chi-restraints excluded: chain A residue  742 ASP
Chi-restraints excluded: chain A residue  803 THR
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  810 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 117 optimal weight:    0.2980
   chunk 75 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9990
   chunk 57 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 544 ASN
** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 684 HIS
** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 917 GLN
** B 944 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1098 ASN
A 239 GLN
A 311 ASN
** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 653 ASN
A 681 GLN
A 690 GLN
A 718 GLN
** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.180397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.146502 restraints weight = 31901.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 3.80
r_work: 0.3703 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.1963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10758  Z= 0.183
  Angle     :  0.634   7.959  14524  Z= 0.332
  Chirality :  0.044   0.311   1671
  Planarity :  0.004   0.036   1844
  Dihedral  :  9.090  87.457   1494
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 21.93 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.34 (0.23), residues: 1306
  helix:  0.15 (0.19), residues: 716
  sheet: -2.48 (0.43), residues: 118
  loop : -2.00 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 638 
 TYR   0.022   0.002   TYR A 815 
 PHE   0.019   0.002   PHE A 436 
 TRP   0.009   0.001   TRP A 764 
 HIS   0.014   0.001   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (10758)
  covalent geometry    : angle       0.63419 (14524)
  hydrogen bonds       : bond        0.04404 (  553)
  hydrogen bonds       : angle       4.70657 ( 1589)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 272
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  534 PHE cc_start: 0.8198 (m-80) cc_final: 0.7989 (m-80)
REVERT: B  565 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6912 (t0)
REVERT: B  779 ARG cc_start: 0.6287 (mtm-85) cc_final: 0.5963 (mtm180)
REVERT: B  809 ASP cc_start: 0.7334 (t0) cc_final: 0.7005 (t0)
REVERT: B  852 GLN cc_start: 0.8410 (mt0) cc_final: 0.8173 (mt0)
REVERT: B  856 LYS cc_start: 0.8395 (tttt) cc_final: 0.8114 (tttp)
REVERT: B  949 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7356 (mtm110)
REVERT: B  953 MET cc_start: 0.7965 (tpt) cc_final: 0.7699 (tpt)
REVERT: B  975 ASP cc_start: 0.8272 (t0) cc_final: 0.6825 (m-30)
REVERT: B 1077 ASP cc_start: 0.7671 (t0) cc_final: 0.7215 (t0)
REVERT: B 1084 LYS cc_start: 0.7926 (tptp) cc_final: 0.7467 (tptp)
REVERT: B 1092 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7602 (mt-10)
REVERT: B 1103 ARG cc_start: 0.7579 (mtt180) cc_final: 0.6899 (mtt-85)
REVERT: A  172 LYS cc_start: 0.7370 (tttp) cc_final: 0.7057 (mmmt)
REVERT: A  188 GLU cc_start: 0.6552 (tm-30) cc_final: 0.6267 (tm-30)
REVERT: A  253 MET cc_start: 0.6573 (tpt) cc_final: 0.5522 (tpt)
REVERT: A  351 MET cc_start: 0.7757 (mmm) cc_final: 0.7388 (mmm)
REVERT: A  414 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7921 (mp)
REVERT: A  442 ASP cc_start: 0.7999 (t70) cc_final: 0.7658 (t0)
REVERT: A  666 ILE cc_start: 0.8085 (mt) cc_final: 0.6979 (tp)
REVERT: A  720 LYS cc_start: 0.7618 (mttt) cc_final: 0.7406 (mttt)
REVERT: A  726 MET cc_start: 0.8108 (tpp) cc_final: 0.7774 (tpp)
REVERT: A  793 GLN cc_start: 0.7870 (mt0) cc_final: 0.7605 (tt0)
REVERT: A  845 LYS cc_start: 0.8026 (mtpt) cc_final: 0.7710 (mtmm)
REVERT: A  846 GLN cc_start: 0.7684 (mp10) cc_final: 0.7415 (mp10)
  outliers start: 37
  outliers final: 24
  residues processed: 294
  average time/residue: 0.1293
  time to fit residues: 51.2033
Evaluate side-chains
  283 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 257
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  565 ASP
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  642 VAL
Chi-restraints excluded: chain B residue  644 THR
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  744 TYR
Chi-restraints excluded: chain B residue  882 THR
Chi-restraints excluded: chain B residue  965 LYS
Chi-restraints excluded: chain B residue 1025 VAL
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain A residue  732 THR
Chi-restraints excluded: chain A residue  742 ASP
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9980
   chunk 45 optimal weight:    0.2980
   chunk 5 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 104 optimal weight:    0.1980
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 684 HIS
** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 944 ASN
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 GLN
** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 653 ASN
** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 681 GLN
** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.180625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.147000 restraints weight = 35475.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 4.11
r_work: 0.3697 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3703
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3703 r_free = 0.3703    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3703 r_free = 0.3703    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3703
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.2274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10758  Z= 0.172
  Angle     :  0.615   7.233  14524  Z= 0.321
  Chirality :  0.043   0.260   1671
  Planarity :  0.004   0.044   1844
  Dihedral  :  8.851  86.756   1487
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 22.01 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.10 (0.23), residues: 1306
  helix:  0.34 (0.19), residues: 718
  sheet: -2.34 (0.44), residues: 118
  loop : -1.90 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 737 
 TYR   0.020   0.002   TYR A 619 
 PHE   0.024   0.002   PHE A 436 
 TRP   0.009   0.001   TRP B 807 
 HIS   0.016   0.001   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (10758)
  covalent geometry    : angle       0.61463 (14524)
  hydrogen bonds       : bond        0.04225 (  553)
  hydrogen bonds       : angle       4.58533 ( 1589)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 271
  time to evaluate  : 0.349 
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: B  565 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6877 (t0)
REVERT: B  779 ARG cc_start: 0.6331 (mtm-85) cc_final: 0.6015 (mtm180)
REVERT: B  809 ASP cc_start: 0.7340 (t0) cc_final: 0.7013 (t0)
REVERT: B  852 GLN cc_start: 0.8394 (mt0) cc_final: 0.8183 (mt0)
REVERT: B  856 LYS cc_start: 0.8361 (tttt) cc_final: 0.8114 (tttp)
REVERT: B  889 GLU cc_start: 0.7718 (pm20) cc_final: 0.7414 (pt0)
REVERT: B  944 ASN cc_start: 0.7382 (t0) cc_final: 0.6985 (t0)
REVERT: B  949 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7425 (mtm110)
REVERT: B  953 MET cc_start: 0.7933 (tpt) cc_final: 0.7049 (tpt)
REVERT: B 1077 ASP cc_start: 0.7632 (t0) cc_final: 0.7096 (t0)
REVERT: B 1084 LYS cc_start: 0.7915 (tptp) cc_final: 0.7465 (tptp)
REVERT: B 1092 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7665 (mt-10)
REVERT: A  172 LYS cc_start: 0.7431 (tttp) cc_final: 0.7143 (mmtt)
REVERT: A  188 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6312 (tm-30)
REVERT: A  253 MET cc_start: 0.6425 (tpt) cc_final: 0.5498 (tpt)
REVERT: A  351 MET cc_start: 0.7776 (mmm) cc_final: 0.7496 (tpp)
REVERT: A  358 GLU cc_start: 0.7793 (tt0) cc_final: 0.7518 (pp20)
REVERT: A  414 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7902 (mp)
REVERT: A  442 ASP cc_start: 0.7993 (t70) cc_final: 0.7638 (t0)
REVERT: A  492 MET cc_start: 0.5015 (tmm) cc_final: 0.3545 (ttp)
REVERT: A  702 VAL cc_start: 0.8841 (t) cc_final: 0.8628 (m)
REVERT: A  720 LYS cc_start: 0.7620 (mttt) cc_final: 0.7419 (mttt)
REVERT: A  726 MET cc_start: 0.8072 (tpp) cc_final: 0.7739 (tpp)
REVERT: A  768 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6975 (pp20)
REVERT: A  793 GLN cc_start: 0.7998 (mt0) cc_final: 0.7711 (tt0)
REVERT: A  845 LYS cc_start: 0.8055 (mtpt) cc_final: 0.7721 (mtmm)
REVERT: A  846 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7478 (mp10)
  outliers start: 44
  outliers final: 28
  residues processed: 296
  average time/residue: 0.1231
  time to fit residues: 48.8145
Evaluate side-chains
  293 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 261
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  565 ASP
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  642 VAL
Chi-restraints excluded: chain B residue  644 THR
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  692 GLN
Chi-restraints excluded: chain B residue  744 TYR
Chi-restraints excluded: chain B residue  882 THR
Chi-restraints excluded: chain B residue  925 GLU
Chi-restraints excluded: chain B residue  965 LYS
Chi-restraints excluded: chain B residue 1000 ASP
Chi-restraints excluded: chain B residue 1025 VAL
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain B residue 1094 GLU
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  741 LYS
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  846 GLN
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 100 optimal weight:    0.9980
   chunk 87 optimal weight:    5.9990
   chunk 78 optimal weight:    0.7980
   chunk 14 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 684 HIS
** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1088 HIS
B1098 ASN
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 536 ASN
A 653 ASN
** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 681 GLN
** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.179786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.148679 restraints weight = 19670.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 2.49
r_work: 0.3789 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3797
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3797 r_free = 0.3797    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3797 r_free = 0.3797    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3797
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7041
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10758  Z= 0.197
  Angle     :  0.613   6.792  14524  Z= 0.320
  Chirality :  0.044   0.231   1671
  Planarity :  0.004   0.039   1844
  Dihedral  :  8.830  87.892   1485
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 21.93 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.23), residues: 1306
  helix:  0.38 (0.19), residues: 725
  sheet: -2.16 (0.45), residues: 118
  loop : -1.79 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 737 
 TYR   0.019   0.002   TYR A 815 
 PHE   0.028   0.002   PHE A 436 
 TRP   0.007   0.001   TRP B 768 
 HIS   0.015   0.001   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (10758)
  covalent geometry    : angle       0.61341 (14524)
  hydrogen bonds       : bond        0.04181 (  553)
  hydrogen bonds       : angle       4.54748 ( 1589)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 263
  time to evaluate  : 0.465 
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: B  779 ARG cc_start: 0.6223 (mtm-85) cc_final: 0.5949 (mtm180)
REVERT: B  809 ASP cc_start: 0.7301 (t0) cc_final: 0.6964 (t0)
REVERT: B  852 GLN cc_start: 0.8233 (mt0) cc_final: 0.7860 (mt0)
REVERT: B  856 LYS cc_start: 0.8236 (tttt) cc_final: 0.7870 (tttm)
REVERT: B  902 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7871 (mtmm)
REVERT: B  944 ASN cc_start: 0.7285 (t0) cc_final: 0.6987 (t0)
REVERT: B 1077 ASP cc_start: 0.7491 (t0) cc_final: 0.7154 (t0)
REVERT: B 1084 LYS cc_start: 0.7794 (tptp) cc_final: 0.7335 (tptp)
REVERT: A  172 LYS cc_start: 0.7414 (tttp) cc_final: 0.7073 (mmmt)
REVERT: A  188 GLU cc_start: 0.6555 (tm-30) cc_final: 0.6334 (tm-30)
REVERT: A  253 MET cc_start: 0.6273 (tpt) cc_final: 0.5356 (tpt)
REVERT: A  358 GLU cc_start: 0.7596 (tt0) cc_final: 0.7338 (pp20)
REVERT: A  442 ASP cc_start: 0.7928 (t70) cc_final: 0.7551 (t0)
REVERT: A  666 ILE cc_start: 0.8145 (mm) cc_final: 0.7652 (mt)
REVERT: A  702 VAL cc_start: 0.8807 (t) cc_final: 0.8577 (m)
REVERT: A  726 MET cc_start: 0.7895 (tpp) cc_final: 0.7513 (tpp)
REVERT: A  779 MET cc_start: 0.6752 (tpp) cc_final: 0.6549 (ttm)
REVERT: A  793 GLN cc_start: 0.7878 (mt0) cc_final: 0.7563 (tt0)
REVERT: A  845 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7631 (mtmm)
REVERT: A  846 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7322 (mp10)
  outliers start: 46
  outliers final: 34
  residues processed: 287
  average time/residue: 0.1274
  time to fit residues: 49.7688
Evaluate side-chains
  297 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 261
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  565 ASP
Chi-restraints excluded: chain B residue  577 LYS
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  642 VAL
Chi-restraints excluded: chain B residue  644 THR
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  692 GLN
Chi-restraints excluded: chain B residue  744 TYR
Chi-restraints excluded: chain B residue  794 GLN
Chi-restraints excluded: chain B residue  799 LEU
Chi-restraints excluded: chain B residue  882 THR
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  902 LYS
Chi-restraints excluded: chain B residue  917 GLN
Chi-restraints excluded: chain B residue  925 GLU
Chi-restraints excluded: chain B residue  965 LYS
Chi-restraints excluded: chain B residue 1000 ASP
Chi-restraints excluded: chain B residue 1025 VAL
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  741 LYS
Chi-restraints excluded: chain A residue  742 ASP
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  846 GLN
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 67 optimal weight:    0.9990
   chunk 108 optimal weight:    0.2980
   chunk 61 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 97 optimal weight:    0.0870
   chunk 112 optimal weight:    0.9980
   chunk 90 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 111 optimal weight:    0.8980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** B 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 861 ASN
** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 GLN
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 681 GLN
** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.182008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.147785 restraints weight = 32122.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 3.92
r_work: 0.3731 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3735
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3735 r_free = 0.3735    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3735 r_free = 0.3735    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3735
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10758  Z= 0.156
  Angle     :  0.593   7.480  14524  Z= 0.308
  Chirality :  0.043   0.366   1671
  Planarity :  0.004   0.039   1844
  Dihedral  :  8.695  84.412   1485
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 22.18 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.77 (0.23), residues: 1306
  helix:  0.56 (0.19), residues: 725
  sheet: -2.24 (0.43), residues: 125
  loop : -1.67 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 999 
 TYR   0.020   0.002   TYR A 815 
 PHE   0.032   0.002   PHE B 534 
 TRP   0.007   0.001   TRP B1122 
 HIS   0.010   0.001   HIS B 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (10758)
  covalent geometry    : angle       0.59272 (14524)
  hydrogen bonds       : bond        0.03940 (  553)
  hydrogen bonds       : angle       4.45297 ( 1589)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 266
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  809 ASP cc_start: 0.7354 (t0) cc_final: 0.7028 (t0)
REVERT: B  856 LYS cc_start: 0.8310 (tttt) cc_final: 0.8098 (tttp)
REVERT: B  944 ASN cc_start: 0.7439 (t0) cc_final: 0.7123 (t0)
REVERT: B  953 MET cc_start: 0.7821 (tpt) cc_final: 0.6994 (tpt)
REVERT: B  975 ASP cc_start: 0.8302 (t0) cc_final: 0.6784 (m-30)
REVERT: B 1077 ASP cc_start: 0.7612 (t0) cc_final: 0.7299 (t0)
REVERT: B 1084 LYS cc_start: 0.7873 (tptp) cc_final: 0.7432 (tptp)
REVERT: A  172 LYS cc_start: 0.7522 (tttp) cc_final: 0.7167 (mmmt)
REVERT: A  188 GLU cc_start: 0.6576 (tm-30) cc_final: 0.6286 (tm-30)
REVERT: A  253 MET cc_start: 0.6231 (tpt) cc_final: 0.5393 (tpt)
REVERT: A  383 ARG cc_start: 0.7126 (mtt180) cc_final: 0.6889 (mtt90)
REVERT: A  414 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7873 (mp)
REVERT: A  442 ASP cc_start: 0.8004 (t70) cc_final: 0.7646 (t0)
REVERT: A  492 MET cc_start: 0.5007 (tmm) cc_final: 0.3537 (ttp)
REVERT: A  702 VAL cc_start: 0.8807 (t) cc_final: 0.8604 (m)
REVERT: A  720 LYS cc_start: 0.7514 (mttt) cc_final: 0.7308 (mttm)
REVERT: A  726 MET cc_start: 0.8104 (tpp) cc_final: 0.7746 (tpp)
REVERT: A  729 MET cc_start: 0.7989 (mmp) cc_final: 0.7722 (mmm)
REVERT: A  758 ASP cc_start: 0.7814 (t0) cc_final: 0.7482 (t0)
REVERT: A  768 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6976 (pp20)
REVERT: A  779 MET cc_start: 0.6888 (tpp) cc_final: 0.6631 (tpp)
REVERT: A  793 GLN cc_start: 0.7976 (mt0) cc_final: 0.7684 (tt0)
REVERT: A  845 LYS cc_start: 0.8010 (mtpt) cc_final: 0.7697 (mtmm)
REVERT: A  846 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7485 (mp10)
  outliers start: 41
  outliers final: 29
  residues processed: 289
  average time/residue: 0.1236
  time to fit residues: 48.6823
Evaluate side-chains
  286 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 254
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  577 LYS
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  642 VAL
Chi-restraints excluded: chain B residue  644 THR
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  744 TYR
Chi-restraints excluded: chain B residue  794 GLN
Chi-restraints excluded: chain B residue  799 LEU
Chi-restraints excluded: chain B residue  882 THR
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  965 LYS
Chi-restraints excluded: chain B residue 1025 VAL
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain A residue  148 VAL
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  741 LYS
Chi-restraints excluded: chain A residue  742 ASP
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  846 GLN
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 56 optimal weight:    0.0270
   chunk 35 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 123 optimal weight:    0.2980
   chunk 49 optimal weight:    0.8980
   chunk 126 optimal weight:    5.9990
   chunk 32 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0770
   overall best weight:    0.3396

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

Flipped N/Q/H residues before XYZ refinement:
B 684 HIS
** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1098 ASN
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 798 ASN ** 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 = 0.4368 r_free = 0.4368 target = 0.183528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.150554 restraints weight = 23497.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 2.87
r_work: 0.3811 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3815
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3815 r_free = 0.3815    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3815 r_free = 0.3815    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3815
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10758  Z= 0.134
  Angle     :  0.594   7.740  14524  Z= 0.306
  Chirality :  0.042   0.310   1671
  Planarity :  0.004   0.037   1844
  Dihedral  :  8.437  81.667   1484
  Min Nonbonded Distance : 1.859

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 23.21 %
    Favored  : 73.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.23), residues: 1306
  helix:  0.76 (0.19), residues: 719
  sheet: -2.41 (0.39), residues: 148
  loop : -1.53 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 938 
 TYR   0.024   0.002   TYR A 815 
 PHE   0.030   0.002   PHE A 760 
 TRP   0.007   0.001   TRP A 764 
 HIS   0.005   0.001   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (10758)
  covalent geometry    : angle       0.59352 (14524)
  hydrogen bonds       : bond        0.03762 (  553)
  hydrogen bonds       : angle       4.36061 ( 1589)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 269
  time to evaluate  : 0.446 
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: B  692 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8319 (mp10)
REVERT: B  809 ASP cc_start: 0.7265 (t0) cc_final: 0.6955 (t0)
REVERT: B  856 LYS cc_start: 0.8083 (tttt) cc_final: 0.7849 (tttm)
REVERT: B  877 TYR cc_start: 0.8329 (t80) cc_final: 0.7292 (t80)
REVERT: B  881 ASN cc_start: 0.7761 (m-40) cc_final: 0.7557 (m-40)
REVERT: B  944 ASN cc_start: 0.7343 (t0) cc_final: 0.7025 (t0)
REVERT: B  975 ASP cc_start: 0.8251 (t0) cc_final: 0.6720 (m-30)
REVERT: B 1077 ASP cc_start: 0.7507 (t0) cc_final: 0.7296 (t0)
REVERT: B 1084 LYS cc_start: 0.7815 (tptp) cc_final: 0.7376 (tptp)
REVERT: A  172 LYS cc_start: 0.7464 (tttp) cc_final: 0.7108 (mmmt)
REVERT: A  188 GLU cc_start: 0.6488 (tm-30) cc_final: 0.6235 (tm-30)
REVERT: A  253 MET cc_start: 0.6046 (tpt) cc_final: 0.5283 (tpt)
REVERT: A  355 ARG cc_start: 0.7415 (mtm180) cc_final: 0.7010 (ttp-110)
REVERT: A  358 GLU cc_start: 0.7623 (tt0) cc_final: 0.7160 (pt0)
REVERT: A  383 ARG cc_start: 0.6915 (mtt180) cc_final: 0.6677 (mtt90)
REVERT: A  402 GLN cc_start: 0.7705 (tt0) cc_final: 0.7500 (tp40)
REVERT: A  414 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7758 (mp)
REVERT: A  442 ASP cc_start: 0.7918 (t70) cc_final: 0.7569 (t0)
REVERT: A  492 MET cc_start: 0.5014 (tmm) cc_final: 0.3550 (ttp)
REVERT: A  691 ILE cc_start: 0.8136 (tt) cc_final: 0.7689 (pt)
REVERT: A  720 LYS cc_start: 0.7378 (mttt) cc_final: 0.7079 (mttm)
REVERT: A  726 MET cc_start: 0.7988 (tpp) cc_final: 0.7600 (tpp)
REVERT: A  729 MET cc_start: 0.7941 (mmp) cc_final: 0.7689 (mmm)
REVERT: A  758 ASP cc_start: 0.7709 (t0) cc_final: 0.7389 (t0)
REVERT: A  768 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6631 (pp20)
REVERT: A  769 TYR cc_start: 0.8214 (t80) cc_final: 0.7534 (t80)
REVERT: A  793 GLN cc_start: 0.7841 (mt0) cc_final: 0.7555 (tt0)
REVERT: A  845 LYS cc_start: 0.7947 (mtpt) cc_final: 0.7600 (mtmm)
REVERT: A  846 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7338 (mp10)
  outliers start: 38
  outliers final: 25
  residues processed: 290
  average time/residue: 0.1235
  time to fit residues: 48.7672
Evaluate side-chains
  282 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 253
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  644 THR
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  692 GLN
Chi-restraints excluded: chain B residue  702 LEU
Chi-restraints excluded: chain B residue  794 GLN
Chi-restraints excluded: chain B residue  799 LEU
Chi-restraints excluded: chain B residue  882 THR
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue 1017 LEU
Chi-restraints excluded: chain B residue 1025 VAL
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain A residue  741 LYS
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  846 GLN
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 56 optimal weight:    0.2980
   chunk 44 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 120 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 95 optimal weight:   10.0000
   chunk 112 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 538 ASN
** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 880 ASN
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1098 ASN
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 288 GLN
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 653 ASN
** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.180789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.147627 restraints weight = 26496.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3908 rms_B_bonded: 3.47
r_work: 0.3723 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3724
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3724 r_free = 0.3724    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3724 r_free = 0.3724    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090  10758  Z= 0.193
  Angle     :  0.629   9.057  14524  Z= 0.324
  Chirality :  0.044   0.303   1671
  Planarity :  0.004   0.040   1844
  Dihedral  :  8.494  83.524   1481
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 14.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 22.78 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.23), residues: 1306
  helix:  0.64 (0.19), residues: 729
  sheet: -2.44 (0.39), residues: 143
  loop : -1.46 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 308 
 TYR   0.029   0.002   TYR A 815 
 PHE   0.035   0.002   PHE A 760 
 TRP   0.008   0.001   TRP A 764 
 HIS   0.005   0.001   HIS B 781 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (10758)
  covalent geometry    : angle       0.62889 (14524)
  hydrogen bonds       : bond        0.03948 (  553)
  hydrogen bonds       : angle       4.45110 ( 1589)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 265
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  692 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8334 (mp10)
REVERT: B  809 ASP cc_start: 0.7398 (t0) cc_final: 0.7050 (t0)
REVERT: B  856 LYS cc_start: 0.8368 (tttt) cc_final: 0.8100 (tttt)
REVERT: B  858 VAL cc_start: 0.8536 (t) cc_final: 0.8241 (m)
REVERT: B  928 THR cc_start: 0.7770 (p) cc_final: 0.7435 (p)
REVERT: B  944 ASN cc_start: 0.7405 (t0) cc_final: 0.7110 (t0)
REVERT: B  949 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7477 (mtm110)
REVERT: B  975 ASP cc_start: 0.8273 (t0) cc_final: 0.6716 (m-30)
REVERT: B 1084 LYS cc_start: 0.7903 (tptp) cc_final: 0.7457 (tptp)
REVERT: B 1091 LYS cc_start: 0.8022 (mmtm) cc_final: 0.7751 (mmtp)
REVERT: B 1092 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7590 (mt-10)
REVERT: A  172 LYS cc_start: 0.7522 (tttp) cc_final: 0.7213 (mmmt)
REVERT: A  188 GLU cc_start: 0.6629 (tm-30) cc_final: 0.6361 (tm-30)
REVERT: A  246 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7527 (ttmt)
REVERT: A  261 MET cc_start: 0.7816 (mmt) cc_final: 0.7006 (mmt)
REVERT: A  355 ARG cc_start: 0.7592 (mtm180) cc_final: 0.7327 (ttp-110)
REVERT: A  383 ARG cc_start: 0.7291 (mtt180) cc_final: 0.6970 (mtt90)
REVERT: A  402 GLN cc_start: 0.7766 (tt0) cc_final: 0.7522 (tp40)
REVERT: A  414 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7843 (mp)
REVERT: A  442 ASP cc_start: 0.8017 (t70) cc_final: 0.7652 (t0)
REVERT: A  691 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7750 (pt)
REVERT: A  720 LYS cc_start: 0.7532 (mttt) cc_final: 0.7210 (mttm)
REVERT: A  726 MET cc_start: 0.8044 (tpp) cc_final: 0.7614 (tpp)
REVERT: A  729 MET cc_start: 0.8084 (mmp) cc_final: 0.7817 (mmm)
REVERT: A  758 ASP cc_start: 0.7789 (t0) cc_final: 0.7495 (t0)
REVERT: A  768 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6976 (pp20)
REVERT: A  793 GLN cc_start: 0.8072 (mt0) cc_final: 0.7742 (tt0)
REVERT: A  845 LYS cc_start: 0.8026 (mtpt) cc_final: 0.7654 (mtmm)
REVERT: A  846 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7432 (mp10)
  outliers start: 40
  outliers final: 30
  residues processed: 290
  average time/residue: 0.1247
  time to fit residues: 48.9696
Evaluate side-chains
  297 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 262
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  565 ASP
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  644 THR
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  692 GLN
Chi-restraints excluded: chain B residue  702 LEU
Chi-restraints excluded: chain B residue  744 TYR
Chi-restraints excluded: chain B residue  794 GLN
Chi-restraints excluded: chain B residue  799 LEU
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  925 GLU
Chi-restraints excluded: chain B residue 1017 LEU
Chi-restraints excluded: chain B residue 1025 VAL
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue  741 LYS
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  846 GLN
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 89 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 123 optimal weight:    0.8980
   chunk 95 optimal weight:    8.9990
   chunk 1 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1098 ASN
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 653 ASN
** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 798 ASN ** 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 = 0.4330 r_free = 0.4330 target = 0.180926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.147572 restraints weight = 30528.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 3.80
r_work: 0.3703 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3706 r_free = 0.3706    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10758  Z= 0.183
  Angle     :  0.641  14.224  14524  Z= 0.328
  Chirality :  0.045   0.350   1671
  Planarity :  0.004   0.039   1844
  Dihedral  :  8.526  79.912   1481
  Min Nonbonded Distance : 1.838

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 23.21 %
    Favored  : 73.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.23), residues: 1306
  helix:  0.64 (0.19), residues: 727
  sheet: -2.30 (0.41), residues: 136
  loop : -1.48 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 308 
 TYR   0.025   0.002   TYR A 815 
 PHE   0.034   0.002   PHE A 760 
 TRP   0.007   0.001   TRP A 764 
 HIS   0.004   0.001   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (10758)
  covalent geometry    : angle       0.64078 (14524)
  hydrogen bonds       : bond        0.03931 (  553)
  hydrogen bonds       : angle       4.45938 ( 1589)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 264
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  692 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.8343 (mp10)
REVERT: B  809 ASP cc_start: 0.7433 (t0) cc_final: 0.7074 (t0)
REVERT: B  856 LYS cc_start: 0.8421 (tttt) cc_final: 0.8142 (tttt)
REVERT: B  858 VAL cc_start: 0.8600 (t) cc_final: 0.8297 (m)
REVERT: B  928 THR cc_start: 0.7794 (p) cc_final: 0.7440 (p)
REVERT: B  944 ASN cc_start: 0.7444 (t0) cc_final: 0.7155 (t0)
REVERT: B  949 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7527 (mtm110)
REVERT: B  975 ASP cc_start: 0.8286 (t0) cc_final: 0.6724 (m-30)
REVERT: B 1034 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7530 (m)
REVERT: B 1084 LYS cc_start: 0.7914 (tptp) cc_final: 0.7459 (tptp)
REVERT: B 1091 LYS cc_start: 0.8020 (mmtm) cc_final: 0.7753 (mmtp)
REVERT: B 1092 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7612 (mt-10)
REVERT: A  172 LYS cc_start: 0.7544 (tttp) cc_final: 0.7069 (mtpp)
REVERT: A  188 GLU cc_start: 0.6619 (tm-30) cc_final: 0.6349 (tm-30)
REVERT: A  355 ARG cc_start: 0.7613 (mtm180) cc_final: 0.7366 (ttp-110)
REVERT: A  383 ARG cc_start: 0.7256 (mtt180) cc_final: 0.6941 (mtt90)
REVERT: A  402 GLN cc_start: 0.7777 (tt0) cc_final: 0.7534 (tp40)
REVERT: A  442 ASP cc_start: 0.8049 (t70) cc_final: 0.7701 (t0)
REVERT: A  453 MET cc_start: 0.7106 (mmt) cc_final: 0.6714 (mmt)
REVERT: A  691 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7928 (pt)
REVERT: A  702 VAL cc_start: 0.8834 (t) cc_final: 0.8634 (m)
REVERT: A  720 LYS cc_start: 0.7560 (mttt) cc_final: 0.7230 (mttm)
REVERT: A  726 MET cc_start: 0.8076 (tpp) cc_final: 0.7650 (tpp)
REVERT: A  729 MET cc_start: 0.8096 (mmp) cc_final: 0.7842 (mmm)
REVERT: A  758 ASP cc_start: 0.7824 (t0) cc_final: 0.7562 (t0)
REVERT: A  768 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7014 (pp20)
REVERT: A  793 GLN cc_start: 0.8076 (mt0) cc_final: 0.7735 (tt0)
REVERT: A  845 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7658 (mtmm)
REVERT: A  846 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7478 (mp10)
  outliers start: 40
  outliers final: 32
  residues processed: 287
  average time/residue: 0.1286
  time to fit residues: 49.5927
Evaluate side-chains
  299 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 262
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  565 ASP
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  644 THR
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  692 GLN
Chi-restraints excluded: chain B residue  744 TYR
Chi-restraints excluded: chain B residue  794 GLN
Chi-restraints excluded: chain B residue  799 LEU
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  925 GLU
Chi-restraints excluded: chain B residue 1017 LEU
Chi-restraints excluded: chain B residue 1025 VAL
Chi-restraints excluded: chain B residue 1034 VAL
Chi-restraints excluded: chain B residue 1072 VAL
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  691 ILE
Chi-restraints excluded: chain A residue  741 LYS
Chi-restraints excluded: chain A residue  742 ASP
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  807 THR
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  846 GLN
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 124 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0970
   chunk 14 optimal weight:    0.0470
   chunk 111 optimal weight:    0.0870
   chunk 10 optimal weight:    1.9990
   chunk 30 optimal weight:    0.4980
   chunk 24 optimal weight:    0.0030
   chunk 54 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 81 optimal weight:    0.5980
   overall best weight:    0.1464

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

Flipped N/Q/H residues before XYZ refinement:
B 729 HIS
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1098 ASN
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 653 ASN
** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.183589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.152808 restraints weight = 19789.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.3981 rms_B_bonded: 2.59
r_work: 0.3839 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3844
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3844 r_free = 0.3844    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3844 r_free = 0.3844    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3844
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10758  Z= 0.123
  Angle     :  0.620  13.482  14524  Z= 0.318
  Chirality :  0.043   0.333   1671
  Planarity :  0.004   0.037   1844
  Dihedral  :  8.361  67.830   1481
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 23.38 %
    Favored  : 73.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.23), residues: 1306
  helix:  0.82 (0.20), residues: 721
  sheet: -2.28 (0.39), residues: 149
  loop : -1.40 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B1066 
 TYR   0.021   0.001   TYR A 815 
 PHE   0.038   0.002   PHE A 760 
 TRP   0.010   0.001   TRP B 579 
 HIS   0.007   0.001   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10758)
  covalent geometry    : angle       0.62049 (14524)
  hydrogen bonds       : bond        0.03705 (  553)
  hydrogen bonds       : angle       4.35120 ( 1589)

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

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

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 262
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  568 LYS cc_start: 0.8247 (mmtt) cc_final: 0.8038 (mmmt)
REVERT: B  809 ASP cc_start: 0.7303 (t0) cc_final: 0.6956 (t0)
REVERT: B  856 LYS cc_start: 0.8125 (tttt) cc_final: 0.7846 (tttt)
REVERT: B  858 VAL cc_start: 0.8486 (t) cc_final: 0.8217 (m)
REVERT: B  928 THR cc_start: 0.7652 (p) cc_final: 0.7306 (p)
REVERT: B  944 ASN cc_start: 0.7259 (t0) cc_final: 0.6956 (t0)
REVERT: B  975 ASP cc_start: 0.8193 (t0) cc_final: 0.6613 (m-30)
REVERT: B  999 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7582 (ttm110)
REVERT: B 1034 VAL cc_start: 0.7570 (OUTLIER) cc_final: 0.7363 (m)
REVERT: B 1084 LYS cc_start: 0.7786 (tptp) cc_final: 0.7304 (tptp)
REVERT: B 1091 LYS cc_start: 0.7811 (mmtm) cc_final: 0.7519 (mmtp)
REVERT: B 1092 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7381 (mt-10)
REVERT: A  172 LYS cc_start: 0.7393 (tttp) cc_final: 0.6975 (mtpp)
REVERT: A  188 GLU cc_start: 0.6467 (tm-30) cc_final: 0.6207 (tm-30)
REVERT: A  332 LYS cc_start: 0.8358 (mmmm) cc_final: 0.8127 (mmmm)
REVERT: A  339 GLN cc_start: 0.7931 (mt0) cc_final: 0.7658 (mt0)
REVERT: A  355 ARG cc_start: 0.7307 (mtm180) cc_final: 0.7091 (ttp-110)
REVERT: A  359 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7800 (ttm170)
REVERT: A  402 GLN cc_start: 0.7629 (tt0) cc_final: 0.7419 (tp40)
REVERT: A  442 ASP cc_start: 0.7901 (t70) cc_final: 0.7546 (t0)
REVERT: A  492 MET cc_start: 0.4987 (tmm) cc_final: 0.3553 (ttp)
REVERT: A  691 ILE cc_start: 0.8082 (tt) cc_final: 0.7555 (pt)
REVERT: A  720 LYS cc_start: 0.7324 (mttt) cc_final: 0.7022 (mttm)
REVERT: A  726 MET cc_start: 0.7900 (tpp) cc_final: 0.7492 (tpp)
REVERT: A  729 MET cc_start: 0.7957 (mmp) cc_final: 0.7692 (mmm)
REVERT: A  758 ASP cc_start: 0.7658 (t0) cc_final: 0.7365 (t0)
REVERT: A  768 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6548 (pp20)
REVERT: A  769 TYR cc_start: 0.8170 (t80) cc_final: 0.7521 (t80)
REVERT: A  793 GLN cc_start: 0.7853 (mt0) cc_final: 0.7560 (tt0)
REVERT: A  845 LYS cc_start: 0.7934 (mtpt) cc_final: 0.7540 (mtmm)
REVERT: A  846 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.7281 (mp10)
  outliers start: 33
  outliers final: 25
  residues processed: 284
  average time/residue: 0.1334
  time to fit residues: 50.7804
Evaluate side-chains
  286 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 258
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  565 ASP
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  644 THR
Chi-restraints excluded: chain B residue  666 ASP
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  673 LEU
Chi-restraints excluded: chain B residue  702 LEU
Chi-restraints excluded: chain B residue  794 GLN
Chi-restraints excluded: chain B residue  799 LEU
Chi-restraints excluded: chain B residue  885 SER
Chi-restraints excluded: chain B residue  917 GLN
Chi-restraints excluded: chain B residue  925 GLU
Chi-restraints excluded: chain B residue 1017 LEU
Chi-restraints excluded: chain B residue 1034 VAL
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  414 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain A residue  633 ILE
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  846 GLN
Chi-restraints excluded: chain A residue  851 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 125 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 100 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0030
   chunk 18 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0970
   chunk 13 optimal weight:    3.9990
   chunk 116 optimal weight:    0.7980
   chunk 9 optimal weight:    0.2980
   overall best weight:    0.3188

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

Flipped N/Q/H residues before XYZ refinement:
B 684 HIS
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1098 ASN
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 653 ASN
** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4362 r_free = 0.4362 target = 0.184420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.152212 restraints weight = 28030.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 3.35
r_work: 0.3777 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3779
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3779 r_free = 0.3779    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10758  Z= 0.134
  Angle     :  0.617  13.381  14524  Z= 0.317
  Chirality :  0.043   0.313   1671
  Planarity :  0.004   0.036   1844
  Dihedral  :  8.214  73.584   1480
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 24.40 %
    Favored  : 73.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.24), residues: 1306
  helix:  0.87 (0.19), residues: 722
  sheet: -2.27 (0.39), residues: 148
  loop : -1.32 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B1066 
 TYR   0.023   0.001   TYR A 815 
 PHE   0.037   0.002   PHE A 760 
 TRP   0.007   0.001   TRP A 764 
 HIS   0.006   0.001   HIS A 424 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10758)
  covalent geometry    : angle       0.61702 (14524)
  hydrogen bonds       : bond        0.03678 (  553)
  hydrogen bonds       : angle       4.31920 ( 1589)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3347.90 seconds
wall clock time: 58 minutes 7.58 seconds (3487.58 seconds total)