Starting phenix.real_space_refine
on Mon Jul 28 22:51:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8omq_16974/07_2025/8omq_16974.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8omq_16974/07_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8omq_16974/07_2025/8omq_16974.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8omq_16974/07_2025/8omq_16974.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8omq_16974/07_2025/8omq_16974.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8omq_16974/07_2025/8omq_16974.cif"
  }
  resolution = 3.11
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.47, per 1000 atoms: 1.08
  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: 2.40
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  

  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: 1.06
  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: 3.24

  Time building geometry restraints manager: 2.91 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:             1.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     32.890
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.070
  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:             0.010
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.380
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.017   0.004   TRP B 579 
 HIS   0.013   0.002   HIS A 610 
 PHE   0.014   0.003   PHE A 836 
 TYR   0.018   0.003   TYR A 405 
 ARG   0.005   0.001   ARG A 680 

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

*********************** 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  : 1.224 
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: 0.3089
  time to fit residues: 139.9903
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  : 1.175 
-------------------------------------------------------------------------------
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 110 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 66 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 102 optimal weight:    0.0030
   chunk 39 optimal weight:    0.2980
   chunk 62 optimal weight:    0.6980
   chunk 76 optimal weight:    0.7980
   chunk 118 optimal weight:    0.5980
   overall best weight:    0.3990

-------------------------------------------------------------------------------
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
B1114 HIS
** 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 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 21

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.181632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.147035 restraints weight = 26396.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.3908 rms_B_bonded: 3.13
r_work: 0.3739 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3743
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3743 r_free = 0.3743    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3743 r_free = 0.3743    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3743
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.1631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10758  Z= 0.161
  Angle     :  0.657   8.822  14524  Z= 0.344
  Chirality :  0.043   0.255   1671
  Planarity :  0.004   0.039   1844
  Dihedral  :  9.533  87.680   1511
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 14.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 20.14 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.75 (0.22), residues: 1306
  helix: -0.19 (0.19), residues: 719
  sheet: -2.76 (0.42), residues: 118
  loop : -2.16 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 562 
 HIS   0.017   0.002   HIS B 614 
 PHE   0.031   0.002   PHE A 286 
 TYR   0.027   0.002   TYR A 815 
 ARG   0.008   0.001   ARG A 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04583 (  553)
  hydrogen bonds       : angle       4.89374 ( 1589)
  covalent geometry    : bond        0.00361 (10758)
  covalent geometry    : angle       0.65745 (14524)

*********************** 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
  328 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 286
  time to evaluate  : 1.371 
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  534 PHE cc_start: 0.8183 (m-80) cc_final: 0.7630 (m-80)
REVERT: B  554 MET cc_start: 0.8176 (mmt) cc_final: 0.7956 (mmm)
REVERT: B  557 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8364 (tptp)
REVERT: B  565 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6877 (t0)
REVERT: B  651 GLU cc_start: 0.7782 (tt0) cc_final: 0.7561 (tt0)
REVERT: B  809 ASP cc_start: 0.7238 (t0) cc_final: 0.6945 (t0)
REVERT: B  814 PHE cc_start: 0.8022 (t80) cc_final: 0.7814 (t80)
REVERT: B  852 GLN cc_start: 0.8339 (mt0) cc_final: 0.8091 (mt0)
REVERT: B  858 VAL cc_start: 0.8577 (t) cc_final: 0.8309 (m)
REVERT: B  949 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7075 (mtm110)
REVERT: B  953 MET cc_start: 0.8006 (tpt) cc_final: 0.7448 (tpt)
REVERT: B  975 ASP cc_start: 0.8195 (t0) cc_final: 0.6895 (m-30)
REVERT: B 1072 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7995 (p)
REVERT: B 1077 ASP cc_start: 0.7736 (t0) cc_final: 0.7379 (t0)
REVERT: B 1084 LYS cc_start: 0.7887 (tptp) cc_final: 0.7451 (tptp)
REVERT: B 1092 GLU cc_start: 0.7874 (tt0) cc_final: 0.7642 (mt-10)
REVERT: B 1103 ARG cc_start: 0.7609 (mtt180) cc_final: 0.6951 (mtt-85)
REVERT: A  151 LYS cc_start: 0.8308 (tttt) cc_final: 0.7863 (ttpt)
REVERT: A  172 LYS cc_start: 0.7283 (tttp) cc_final: 0.6971 (mmmt)
REVERT: A  188 GLU cc_start: 0.6396 (tm-30) cc_final: 0.6165 (tm-30)
REVERT: A  244 LEU cc_start: 0.7083 (tp) cc_final: 0.6670 (tp)
REVERT: A  246 LYS cc_start: 0.7710 (ttmt) cc_final: 0.7117 (ttmt)
REVERT: A  351 MET cc_start: 0.7624 (mmm) cc_final: 0.7280 (mmm)
REVERT: A  358 GLU cc_start: 0.7800 (tt0) cc_final: 0.7249 (pt0)
REVERT: A  359 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7722 (mtt180)
REVERT: A  369 ASP cc_start: 0.7483 (m-30) cc_final: 0.7271 (m-30)
REVERT: A  414 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7836 (mp)
REVERT: A  442 ASP cc_start: 0.7854 (t70) cc_final: 0.7595 (t0)
REVERT: A  620 VAL cc_start: 0.8559 (t) cc_final: 0.8316 (m)
REVERT: A  666 ILE cc_start: 0.8191 (mt) cc_final: 0.7086 (tp)
REVERT: A  720 LYS cc_start: 0.7592 (mttt) cc_final: 0.7386 (mttm)
REVERT: A  726 MET cc_start: 0.8108 (tpp) cc_final: 0.7703 (tpp)
REVERT: A  793 GLN cc_start: 0.7906 (mt0) cc_final: 0.7594 (tt0)
REVERT: A  819 LYS cc_start: 0.8129 (tttm) cc_final: 0.7862 (tptt)
REVERT: A  845 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7718 (mtmm)
  outliers start: 42
  outliers final: 25
  residues processed: 312
  average time/residue: 0.3942
  time to fit residues: 165.9929
Evaluate side-chains
  301 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 272
  time to evaluate  : 2.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  557 LYS
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  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  542 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 98 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 0 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 84 optimal weight:    0.3980
   chunk 91 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 121 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 129 optimal weight:    8.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
B 544 ASN
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**
B1088 HIS
B1098 ASN
A 239 GLN
** A 311 ASN ** 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 681 GLN
** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 718 GLN
** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.179289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.146513 restraints weight = 23198.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 2.82
r_work: 0.3743 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3751 r_free = 0.3751    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3751 r_free = 0.3751    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.1943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  10758  Z= 0.239
  Angle     :  0.664   8.555  14524  Z= 0.348
  Chirality :  0.045   0.318   1671
  Planarity :  0.004   0.037   1844
  Dihedral  :  9.245  89.548   1492
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 21.33 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.23), residues: 1306
  helix:  0.01 (0.19), residues: 724
  sheet: -2.62 (0.41), residues: 120
  loop : -2.03 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 807 
 HIS   0.008   0.001   HIS B 614 
 PHE   0.024   0.002   PHE A 436 
 TYR   0.025   0.002   TYR A 815 
 ARG   0.006   0.001   ARG B 999 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04546 (  553)
  hydrogen bonds       : angle       4.79537 ( 1589)
  covalent geometry    : bond        0.00531 (10758)
  covalent geometry    : angle       0.66388 (14524)

*********************** 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
  311 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 269
  time to evaluate  : 1.736 
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: 0.8201 (m-80) cc_final: 0.7957 (m-80)
REVERT: B  565 ASP cc_start: 0.7149 (OUTLIER) cc_final: 0.6940 (t0)
REVERT: B  651 GLU cc_start: 0.7742 (tt0) cc_final: 0.7438 (tt0)
REVERT: B  753 MET cc_start: 0.0920 (ptt) cc_final: -0.1529 (ptt)
REVERT: B  809 ASP cc_start: 0.7307 (t0) cc_final: 0.6981 (t0)
REVERT: B  852 GLN cc_start: 0.8327 (mt0) cc_final: 0.8069 (mt0)
REVERT: B  856 LYS cc_start: 0.8366 (tttt) cc_final: 0.8060 (tttp)
REVERT: B  949 ARG cc_start: 0.7649 (mtm-85) cc_final: 0.7319 (mtm110)
REVERT: B  953 MET cc_start: 0.7912 (tpt) cc_final: 0.7005 (tpt)
REVERT: B 1077 ASP cc_start: 0.7586 (t0) cc_final: 0.7102 (t0)
REVERT: B 1084 LYS cc_start: 0.7843 (tptp) cc_final: 0.7385 (tptp)
REVERT: B 1092 GLU cc_start: 0.7885 (tt0) cc_final: 0.7438 (mt-10)
REVERT: B 1103 ARG cc_start: 0.7560 (mtt180) cc_final: 0.6891 (mtt-85)
REVERT: A  151 LYS cc_start: 0.8283 (tttt) cc_final: 0.7775 (ttpp)
REVERT: A  172 LYS cc_start: 0.7362 (tttp) cc_final: 0.7096 (mmtt)
REVERT: A  188 GLU cc_start: 0.6501 (tm-30) cc_final: 0.6219 (tm-30)
REVERT: A  300 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7911 (ttp)
REVERT: A  351 MET cc_start: 0.7752 (mmm) cc_final: 0.7435 (tpp)
REVERT: A  369 ASP cc_start: 0.7623 (m-30) cc_final: 0.7403 (m-30)
REVERT: A  442 ASP cc_start: 0.8005 (t70) cc_final: 0.7677 (t0)
REVERT: A  666 ILE cc_start: 0.8038 (mt) cc_final: 0.6937 (tp)
REVERT: A  702 VAL cc_start: 0.8816 (t) cc_final: 0.8601 (m)
REVERT: A  720 LYS cc_start: 0.7700 (mttt) cc_final: 0.7495 (mttm)
REVERT: A  726 MET cc_start: 0.7975 (tpp) cc_final: 0.7595 (tpp)
REVERT: A  729 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7790 (mmm)
REVERT: A  793 GLN cc_start: 0.7857 (mt0) cc_final: 0.7559 (tt0)
REVERT: A  819 LYS cc_start: 0.8149 (tttm) cc_final: 0.7805 (tptt)
REVERT: A  845 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7719 (mtmm)
REVERT: A  846 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7357 (mp10)
  outliers start: 42
  outliers final: 30
  residues processed: 292
  average time/residue: 0.2995
  time to fit residues: 117.8803
Evaluate side-chains
  295 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 261
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
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  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 1017 LEU
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  300 MET
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  598 VAL
Chi-restraints excluded: chain A residue  729 MET
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  815 TYR
Chi-restraints excluded: chain A residue  818 LYS
Chi-restraints excluded: chain A residue  846 GLN
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 49 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0370
   chunk 65 optimal weight:    0.8980
   chunk 106 optimal weight:    0.0570
   chunk 50 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 116 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.4376

-------------------------------------------------------------------------------
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 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 944 ASN
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 GLN
A 311 ASN
** 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 783 HIS
** 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 = 0.4341 r_free = 0.4341 target = 0.181719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.149952 restraints weight = 20001.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3945 rms_B_bonded: 2.55
r_work: 0.3800 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3804
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3804 r_free = 0.3804    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3804 r_free = 0.3804    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3804
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7022
moved from start:          0.2326

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= 0.151
  Angle     :  0.610   7.321  14524  Z= 0.317
  Chirality :  0.043   0.269   1671
  Planarity :  0.004   0.036   1844
  Dihedral  :  8.751  83.987   1485
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 14.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.23), residues: 1306
  helix:  0.35 (0.19), residues: 717
  sheet: -2.33 (0.44), residues: 119
  loop : -1.91 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B1122 
 HIS   0.010   0.001   HIS B 614 
 PHE   0.032   0.002   PHE B 814 
 TYR   0.021   0.002   TYR A 815 
 ARG   0.007   0.001   ARG B1066 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04138 (  553)
  hydrogen bonds       : angle       4.62366 ( 1589)
  covalent geometry    : bond        0.00336 (10758)
  covalent geometry    : angle       0.61045 (14524)

*********************** 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
  308 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 267
  time to evaluate  : 1.706 
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  555 LYS cc_start: 0.7885 (mtmm) cc_final: 0.7480 (mtmm)
REVERT: B  565 ASP cc_start: 0.6981 (m-30) cc_final: 0.6744 (t0)
REVERT: B  651 GLU cc_start: 0.7624 (tt0) cc_final: 0.7243 (tt0)
REVERT: B  809 ASP cc_start: 0.7262 (t0) cc_final: 0.6914 (t0)
REVERT: B  852 GLN cc_start: 0.8283 (mt0) cc_final: 0.8052 (mt0)
REVERT: B  856 LYS cc_start: 0.8234 (tttt) cc_final: 0.7976 (tttp)
REVERT: B  949 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7408 (mtm110)
REVERT: B  953 MET cc_start: 0.7871 (tpt) cc_final: 0.7583 (tpt)
REVERT: B 1077 ASP cc_start: 0.7532 (t0) cc_final: 0.7036 (t0)
REVERT: B 1084 LYS cc_start: 0.7787 (tptp) cc_final: 0.7337 (tptp)
REVERT: B 1092 GLU cc_start: 0.7872 (tt0) cc_final: 0.7669 (mt-10)
REVERT: B 1103 ARG cc_start: 0.7553 (mtt180) cc_final: 0.6860 (mtt-85)
REVERT: A  151 LYS cc_start: 0.8233 (tttt) cc_final: 0.7725 (ttpp)
REVERT: A  172 LYS cc_start: 0.7299 (tttp) cc_final: 0.7018 (mmtt)
REVERT: A  188 GLU cc_start: 0.6479 (tm-30) cc_final: 0.6201 (tm-30)
REVERT: A  351 MET cc_start: 0.7673 (mmm) cc_final: 0.7366 (mmm)
REVERT: A  442 ASP cc_start: 0.7936 (t70) cc_final: 0.7546 (t0)
REVERT: A  492 MET cc_start: 0.4998 (tmm) cc_final: 0.3531 (ttp)
REVERT: A  702 VAL cc_start: 0.8789 (t) cc_final: 0.8551 (m)
REVERT: A  726 MET cc_start: 0.7958 (tpp) cc_final: 0.7605 (tpp)
REVERT: A  729 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7738 (mmm)
REVERT: A  768 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6819 (pp20)
REVERT: A  793 GLN cc_start: 0.7831 (mt0) cc_final: 0.7536 (tt0)
REVERT: A  845 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7601 (mtmm)
REVERT: A  846 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7288 (mp10)
  outliers start: 41
  outliers final: 27
  residues processed: 290
  average time/residue: 0.3564
  time to fit residues: 139.6272
Evaluate side-chains
  289 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 259
  time to evaluate  : 1.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  607 VAL
Chi-restraints excluded: chain B residue  628 ILE
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  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 1000 ASP
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 B residue 1094 GLU
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  376 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  768 GLU
Chi-restraints excluded: chain A residue  810 THR
Chi-restraints excluded: chain A residue  815 TYR
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 47 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0270
   chunk 22 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   chunk 101 optimal weight:    0.2980
   chunk 50 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 96 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0370
   chunk 118 optimal weight:    0.9980
   overall best weight:    0.3316

-------------------------------------------------------------------------------
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**
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 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 536 ASN
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.182960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.150200 restraints weight = 24936.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.3947 rms_B_bonded: 2.97
r_work: 0.3789 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3792
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3792 r_free = 0.3792    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3792 r_free = 0.3792    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3792
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.2597

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= 0.136
  Angle     :  0.588   7.134  14524  Z= 0.307
  Chirality :  0.042   0.246   1671
  Planarity :  0.004   0.035   1844
  Dihedral  :  8.446  83.042   1485
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 22.70 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.23), residues: 1306
  helix:  0.60 (0.20), residues: 718
  sheet: -2.32 (0.43), residues: 126
  loop : -1.74 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 768 
 HIS   0.010   0.001   HIS B 614 
 PHE   0.033   0.002   PHE B 534 
 TYR   0.020   0.002   TYR A 815 
 ARG   0.007   0.001   ARG B1066 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03928 (  553)
  hydrogen bonds       : angle       4.44424 ( 1589)
  covalent geometry    : bond        0.00304 (10758)
  covalent geometry    : angle       0.58820 (14524)

*********************** 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
  303 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 265
  time to evaluate  : 1.049 
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  651 GLU cc_start: 0.7573 (tt0) cc_final: 0.7287 (tt0)
REVERT: B  692 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8369 (mp10)
REVERT: B  809 ASP cc_start: 0.7321 (t0) cc_final: 0.6974 (t0)
REVERT: B  852 GLN cc_start: 0.8304 (mt0) cc_final: 0.8076 (mt0)
REVERT: B  856 LYS cc_start: 0.8229 (tttt) cc_final: 0.7970 (tttp)
REVERT: B  944 ASN cc_start: 0.7394 (t0) cc_final: 0.7094 (t0)
REVERT: B  953 MET cc_start: 0.7856 (tpt) cc_final: 0.7616 (tpt)
REVERT: B 1077 ASP cc_start: 0.7569 (t0) cc_final: 0.7303 (t0)
REVERT: B 1084 LYS cc_start: 0.7803 (tptp) cc_final: 0.7339 (tptp)
REVERT: A  151 LYS cc_start: 0.8312 (tttt) cc_final: 0.7820 (ttpp)
REVERT: A  172 LYS cc_start: 0.7339 (tttp) cc_final: 0.7000 (mmmt)
REVERT: A  188 GLU cc_start: 0.6581 (tm-30) cc_final: 0.6354 (tm-30)
REVERT: A  280 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5840 (mt)
REVERT: A  358 GLU cc_start: 0.7664 (tt0) cc_final: 0.7201 (pt0)
REVERT: A  359 ARG cc_start: 0.8061 (ttm170) cc_final: 0.7668 (mtt180)
REVERT: A  442 ASP cc_start: 0.7924 (t70) cc_final: 0.7534 (t0)
REVERT: A  691 ILE cc_start: 0.8073 (mt) cc_final: 0.7833 (tt)
REVERT: A  702 VAL cc_start: 0.8781 (t) cc_final: 0.8554 (m)
REVERT: A  726 MET cc_start: 0.7942 (tpp) cc_final: 0.7597 (tpp)
REVERT: A  729 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7759 (mmm)
REVERT: A  768 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6566 (pp20)
REVERT: A  769 TYR cc_start: 0.8229 (t80) cc_final: 0.7806 (t80)
REVERT: A  793 GLN cc_start: 0.7905 (mt0) cc_final: 0.7595 (tt0)
REVERT: A  845 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7623 (mtmm)
REVERT: A  846 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7299 (mp10)
  outliers start: 38
  outliers final: 24
  residues processed: 287
  average time/residue: 0.3162
  time to fit residues: 124.7989
Evaluate side-chains
  288 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 259
  time to evaluate  : 1.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain B residue  577 LYS
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  587 LEU
Chi-restraints excluded: chain B residue  628 ILE
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  799 LEU
Chi-restraints excluded: chain B residue  882 THR
Chi-restraints excluded: chain B residue  965 LYS
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  280 LEU
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  729 MET
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 111 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 121 optimal weight:    0.0770
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 113 optimal weight:    2.9990
   chunk 41 optimal weight:    0.3980
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
B 729 HIS
B 880 ASN
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1098 ASN
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 ASN
** A 348 GLN ** 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.181285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.150236 restraints weight = 17861.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 2.33
r_work: 0.3823 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3825
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3825 r_free = 0.3825    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3825 r_free = 0.3825    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3825
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7001
moved from start:          0.2653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10758  Z= 0.176
  Angle     :  0.605   7.452  14524  Z= 0.315
  Chirality :  0.043   0.350   1671
  Planarity :  0.004   0.035   1844
  Dihedral  :  8.460  87.520   1482
  Min Nonbonded Distance : 1.830

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 21.59 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.23), residues: 1306
  helix:  0.61 (0.19), residues: 719
  sheet: -2.16 (0.44), residues: 119
  loop : -1.70 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 768 
 HIS   0.009   0.001   HIS B 614 
 PHE   0.028   0.002   PHE B 534 
 TYR   0.022   0.002   TYR A 815 
 ARG   0.007   0.001   ARG B1066 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  553)
  hydrogen bonds       : angle       4.44175 ( 1589)
  covalent geometry    : bond        0.00397 (10758)
  covalent geometry    : angle       0.60488 (14524)

*********************** 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: 40
    poor density    : 267
  time to evaluate  : 1.106 
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  651 GLU cc_start: 0.7491 (tt0) cc_final: 0.7290 (tt0)
REVERT: B  809 ASP cc_start: 0.7280 (t0) cc_final: 0.6954 (t0)
REVERT: B  852 GLN cc_start: 0.8218 (mt0) cc_final: 0.7868 (mt0)
REVERT: B  856 LYS cc_start: 0.8187 (tttt) cc_final: 0.7858 (tttm)
REVERT: B  877 TYR cc_start: 0.8272 (t80) cc_final: 0.7596 (t80)
REVERT: B  902 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7677 (mtmm)
REVERT: B  944 ASN cc_start: 0.7354 (t0) cc_final: 0.7047 (t0)
REVERT: B  949 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7436 (mtm110)
REVERT: B  953 MET cc_start: 0.7848 (tpt) cc_final: 0.6960 (tpt)
REVERT: B 1077 ASP cc_start: 0.7455 (t0) cc_final: 0.7201 (t0)
REVERT: B 1084 LYS cc_start: 0.7772 (tptp) cc_final: 0.7320 (tptp)
REVERT: A  151 LYS cc_start: 0.8284 (tttt) cc_final: 0.7724 (ttpp)
REVERT: A  172 LYS cc_start: 0.7378 (tttp) cc_final: 0.7111 (mmmt)
REVERT: A  188 GLU cc_start: 0.6475 (tm-30) cc_final: 0.6224 (tm-30)
REVERT: A  253 MET cc_start: 0.7141 (ptm) cc_final: 0.6372 (ppp)
REVERT: A  280 LEU cc_start: 0.6015 (OUTLIER) cc_final: 0.5807 (mt)
REVERT: A  413 GLN cc_start: 0.7847 (mm-40) cc_final: 0.7463 (mm-40)
REVERT: A  442 ASP cc_start: 0.7884 (t70) cc_final: 0.7496 (t0)
REVERT: A  492 MET cc_start: 0.4981 (tmm) cc_final: 0.3507 (ttp)
REVERT: A  666 ILE cc_start: 0.8100 (mm) cc_final: 0.7585 (mt)
REVERT: A  702 VAL cc_start: 0.8759 (t) cc_final: 0.8538 (m)
REVERT: A  729 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7734 (mmm)
REVERT: A  793 GLN cc_start: 0.7843 (mt0) cc_final: 0.7533 (tt0)
REVERT: A  845 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7612 (mtmm)
REVERT: A  846 GLN cc_start: 0.7558 (OUTLIER) cc_final: 0.7271 (mp10)
  outliers start: 40
  outliers final: 30
  residues processed: 289
  average time/residue: 0.3704
  time to fit residues: 146.2076
Evaluate side-chains
  291 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 257
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
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  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  794 GLN
Chi-restraints excluded: chain B residue  799 LEU
Chi-restraints excluded: chain B residue  882 THR
Chi-restraints excluded: chain B residue  902 LYS
Chi-restraints excluded: chain B residue  925 GLU
Chi-restraints excluded: chain B residue  965 LYS
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  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  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  596 ASN
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  732 THR
Chi-restraints excluded: chain A residue  742 ASP
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 71 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 89 optimal weight:    9.9990
   chunk 112 optimal weight:    0.8980
   chunk 104 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 130 optimal weight:    0.8980
   chunk 72 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 684 HIS
B 781 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 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 = 0.4333 r_free = 0.4333 target = 0.180711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.149839 restraints weight = 18039.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3946 rms_B_bonded: 2.35
r_work: 0.3814 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3818
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3818 r_free = 0.3818    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3818 r_free = 0.3818    target_work(ls_wunit_k1) = 0.138         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3818
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7013
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  10758  Z= 0.194
  Angle     :  0.628   7.325  14524  Z= 0.324
  Chirality :  0.044   0.325   1671
  Planarity :  0.004   0.059   1844
  Dihedral  :  8.565  87.260   1481
  Min Nonbonded Distance : 1.828

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 21.42 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.23), residues: 1306
  helix:  0.55 (0.19), residues: 724
  sheet: -2.34 (0.42), residues: 129
  loop : -1.61 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 768 
 HIS   0.009   0.001   HIS B 614 
 PHE   0.029   0.002   PHE A 436 
 TYR   0.021   0.002   TYR A 815 
 ARG   0.011   0.001   ARG A 638 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03972 (  553)
  hydrogen bonds       : angle       4.48725 ( 1589)
  covalent geometry    : bond        0.00443 (10758)
  covalent geometry    : angle       0.62825 (14524)

*********************** 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
  311 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 261
  time to evaluate  : 1.098 
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  651 GLU cc_start: 0.7486 (tt0) cc_final: 0.7280 (tt0)
REVERT: B  692 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8277 (mp10)
REVERT: B  809 ASP cc_start: 0.7294 (t0) cc_final: 0.6967 (t0)
REVERT: B  852 GLN cc_start: 0.8198 (mt0) cc_final: 0.7856 (mt0)
REVERT: B  856 LYS cc_start: 0.8204 (tttt) cc_final: 0.7882 (tttm)
REVERT: B  877 TYR cc_start: 0.8243 (t80) cc_final: 0.7628 (t80)
REVERT: B  902 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7852 (mtmm)
REVERT: B  949 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7461 (mtm110)
REVERT: B 1077 ASP cc_start: 0.7417 (t0) cc_final: 0.7157 (t0)
REVERT: B 1084 LYS cc_start: 0.7791 (tptp) cc_final: 0.7335 (tptp)
REVERT: A  151 LYS cc_start: 0.8258 (tttt) cc_final: 0.7781 (ttpp)
REVERT: A  172 LYS cc_start: 0.7412 (tttp) cc_final: 0.7152 (mmmt)
REVERT: A  188 GLU cc_start: 0.6449 (tm-30) cc_final: 0.6201 (tm-30)
REVERT: A  253 MET cc_start: 0.7267 (ptm) cc_final: 0.6411 (ppp)
REVERT: A  442 ASP cc_start: 0.7918 (t70) cc_final: 0.7544 (t0)
REVERT: A  702 VAL cc_start: 0.8770 (t) cc_final: 0.8568 (m)
REVERT: A  726 MET cc_start: 0.7698 (tpp) cc_final: 0.7353 (tpp)
REVERT: A  729 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7734 (mmm)
REVERT: A  768 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6821 (pp20)
REVERT: A  793 GLN cc_start: 0.7863 (mt0) cc_final: 0.7554 (tt0)
REVERT: A  845 LYS cc_start: 0.8013 (mtpt) cc_final: 0.7611 (mtmm)
REVERT: A  846 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7294 (mp10)
  outliers start: 50
  outliers final: 31
  residues processed: 288
  average time/residue: 0.2728
  time to fit residues: 105.6672
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  : 1.089 
-------------------------------------------------------------------------------
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  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  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  925 GLU
Chi-restraints excluded: chain B residue  965 LYS
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  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  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  596 ASN
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  732 THR
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0570
   chunk 96 optimal weight:    9.9990
   chunk 22 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 128 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.7498

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

Flipped N/Q/H residues before XYZ refinement:
** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 861 ASN
** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.179571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.146016 restraints weight = 27975.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 3.15
r_work: 0.3744 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3748 r_free = 0.3748    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3748 r_free = 0.3748    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  10758  Z= 0.193
  Angle     :  0.633   7.292  14524  Z= 0.328
  Chirality :  0.045   0.354   1671
  Planarity :  0.004   0.037   1844
  Dihedral  :  8.483  87.363   1479
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 22.27 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.23), residues: 1306
  helix:  0.56 (0.19), residues: 727
  sheet: -2.37 (0.42), residues: 128
  loop : -1.48 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 768 
 HIS   0.009   0.001   HIS B 614 
 PHE   0.034   0.002   PHE A 760 
 TYR   0.022   0.002   TYR A 815 
 ARG   0.008   0.001   ARG A 638 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  553)
  hydrogen bonds       : angle       4.45509 ( 1589)
  covalent geometry    : bond        0.00439 (10758)
  covalent geometry    : angle       0.63288 (14524)

*********************** 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
  303 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 263
  time to evaluate  : 1.161 
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  809 ASP cc_start: 0.7317 (t0) cc_final: 0.7007 (t0)
REVERT: B  852 GLN cc_start: 0.8300 (mt0) cc_final: 0.7977 (mt0)
REVERT: B  856 LYS cc_start: 0.8284 (tttt) cc_final: 0.7976 (tttm)
REVERT: B  877 TYR cc_start: 0.8304 (t80) cc_final: 0.7584 (t80)
REVERT: B  902 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.8004 (mtmm)
REVERT: B  944 ASN cc_start: 0.7419 (t0) cc_final: 0.7127 (t0)
REVERT: B  949 ARG cc_start: 0.7761 (mtm-85) cc_final: 0.7529 (mtm110)
REVERT: B 1084 LYS cc_start: 0.7851 (tptp) cc_final: 0.7419 (tptp)
REVERT: B 1091 LYS cc_start: 0.7992 (mmtm) cc_final: 0.7735 (mmtp)
REVERT: A  151 LYS cc_start: 0.8373 (tttt) cc_final: 0.7920 (ttpp)
REVERT: A  172 LYS cc_start: 0.7507 (tttp) cc_final: 0.7114 (mtpt)
REVERT: A  188 GLU cc_start: 0.6492 (tm-30) cc_final: 0.6250 (tm-30)
REVERT: A  442 ASP cc_start: 0.7984 (t70) cc_final: 0.7618 (t0)
REVERT: A  726 MET cc_start: 0.7854 (tpp) cc_final: 0.7513 (tpp)
REVERT: A  729 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7811 (mmm)
REVERT: A  758 ASP cc_start: 0.7749 (t0) cc_final: 0.7515 (t0)
REVERT: A  768 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6959 (pp20)
REVERT: A  793 GLN cc_start: 0.7972 (mt0) cc_final: 0.7649 (tt0)
REVERT: A  845 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7664 (mtmm)
REVERT: A  846 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7396 (mp10)
  outliers start: 40
  outliers final: 32
  residues processed: 285
  average time/residue: 0.2735
  time to fit residues: 104.7238
Evaluate side-chains
  293 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 257
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
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  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  666 ASP
Chi-restraints excluded: chain B residue  671 VAL
Chi-restraints excluded: chain B residue  673 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  902 LYS
Chi-restraints excluded: chain B residue  925 GLU
Chi-restraints excluded: chain B residue  965 LYS
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  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  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  596 ASN
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  732 THR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 123 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 111 optimal weight:    0.7980
   chunk 125 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 99 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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
** 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 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 798 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.177964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.144567 restraints weight = 35408.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3886 rms_B_bonded: 3.93
r_work: 0.3675 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  10758  Z= 0.191
  Angle     :  0.641   7.150  14524  Z= 0.331
  Chirality :  0.045   0.303   1671
  Planarity :  0.004   0.036   1844
  Dihedral  :  8.509  87.184   1479
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 22.70 %
    Favored  : 74.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.23), residues: 1306
  helix:  0.57 (0.19), residues: 721
  sheet: -2.45 (0.41), residues: 140
  loop : -1.51 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 768 
 HIS   0.015   0.001   HIS B 614 
 PHE   0.040   0.002   PHE A 760 
 TYR   0.025   0.002   TYR A 815 
 ARG   0.012   0.001   ARG A 638 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04003 (  553)
  hydrogen bonds       : angle       4.46892 ( 1589)
  covalent geometry    : bond        0.00436 (10758)
  covalent geometry    : angle       0.64050 (14524)

*********************** 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: 38
    poor density    : 266
  time to evaluate  : 1.172 
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  809 ASP cc_start: 0.7442 (t0) cc_final: 0.7149 (t0)
REVERT: B  852 GLN cc_start: 0.8402 (mt0) cc_final: 0.8045 (mt0)
REVERT: B  856 LYS cc_start: 0.8332 (tttt) cc_final: 0.8015 (tttm)
REVERT: B  877 TYR cc_start: 0.8364 (t80) cc_final: 0.7641 (t80)
REVERT: B  944 ASN cc_start: 0.7502 (t0) cc_final: 0.7209 (t0)
REVERT: B  949 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7527 (mtm110)
REVERT: B 1084 LYS cc_start: 0.7904 (tptp) cc_final: 0.7459 (tptp)
REVERT: B 1091 LYS cc_start: 0.8030 (mmtm) cc_final: 0.7787 (mmtp)
REVERT: A  151 LYS cc_start: 0.8411 (tttt) cc_final: 0.7948 (ttpp)
REVERT: A  172 LYS cc_start: 0.7551 (tttp) cc_final: 0.7231 (mmmt)
REVERT: A  188 GLU cc_start: 0.6630 (tm-30) cc_final: 0.6390 (tm-30)
REVERT: A  379 ASP cc_start: 0.6977 (m-30) cc_final: 0.6693 (m-30)
REVERT: A  442 ASP cc_start: 0.8073 (t70) cc_final: 0.7717 (t0)
REVERT: A  453 MET cc_start: 0.7157 (mmt) cc_final: 0.6774 (mmt)
REVERT: A  726 MET cc_start: 0.7996 (tpp) cc_final: 0.7772 (tpp)
REVERT: A  729 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7879 (mmm)
REVERT: A  768 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.7060 (pp20)
REVERT: A  793 GLN cc_start: 0.8156 (mt0) cc_final: 0.7808 (tt0)
REVERT: A  845 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7714 (mtmm)
REVERT: A  846 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.7509 (mp10)
  outliers start: 38
  outliers final: 31
  residues processed: 288
  average time/residue: 0.2888
  time to fit residues: 112.3338
Evaluate side-chains
  292 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 258
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
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  587 LEU
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  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  925 GLU
Chi-restraints excluded: chain B residue  965 LYS
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  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  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  596 ASN
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  732 THR
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 94 optimal weight:    0.4980
   chunk 44 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 126 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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**
** 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 402 GLN
** 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**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.180530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.148182 restraints weight = 30632.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3898 rms_B_bonded: 3.63
r_work: 0.3711 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3717 r_free = 0.3717    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.3083

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= 0.182
  Angle     :  0.640   7.167  14524  Z= 0.333
  Chirality :  0.045   0.303   1671
  Planarity :  0.004   0.037   1844
  Dihedral  :  8.552  81.414   1479
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.38 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.23), residues: 1306
  helix:  0.59 (0.19), residues: 721
  sheet: -2.28 (0.42), residues: 130
  loop : -1.57 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 768 
 HIS   0.015   0.001   HIS B 614 
 PHE   0.040   0.002   PHE A 760 
 TYR   0.026   0.002   TYR A 815 
 ARG   0.011   0.001   ARG A 638 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03947 (  553)
  hydrogen bonds       : angle       4.44869 ( 1589)
  covalent geometry    : bond        0.00418 (10758)
  covalent geometry    : angle       0.63983 (14524)

********************** 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
  292 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 257
  time to evaluate  : 1.356 
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  809 ASP cc_start: 0.7376 (t0) cc_final: 0.7083 (t0)
REVERT: B  852 GLN cc_start: 0.8357 (mt0) cc_final: 0.7999 (mt0)
REVERT: B  856 LYS cc_start: 0.8269 (tttt) cc_final: 0.7951 (tttm)
REVERT: B  877 TYR cc_start: 0.8331 (t80) cc_final: 0.7616 (t80)
REVERT: B  944 ASN cc_start: 0.7492 (t0) cc_final: 0.7189 (t0)
REVERT: B  949 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.7488 (mtp85)
REVERT: B 1084 LYS cc_start: 0.7893 (tptp) cc_final: 0.7447 (tptp)
REVERT: B 1091 LYS cc_start: 0.7923 (mmtm) cc_final: 0.7622 (mmtp)
REVERT: A  151 LYS cc_start: 0.8363 (tttt) cc_final: 0.7901 (ttpp)
REVERT: A  172 LYS cc_start: 0.7529 (tttp) cc_final: 0.7209 (mmmt)
REVERT: A  188 GLU cc_start: 0.6631 (tm-30) cc_final: 0.6389 (tm-30)
REVERT: A  358 GLU cc_start: 0.7761 (tt0) cc_final: 0.7435 (tm-30)
REVERT: A  379 ASP cc_start: 0.6915 (m-30) cc_final: 0.6618 (m-30)
REVERT: A  442 ASP cc_start: 0.8046 (t70) cc_final: 0.7685 (t0)
REVERT: A  726 MET cc_start: 0.7938 (tpp) cc_final: 0.7705 (tpp)
REVERT: A  729 MET cc_start: 0.8058 (OUTLIER) cc_final: 0.7831 (mmm)
REVERT: A  758 ASP cc_start: 0.7829 (t0) cc_final: 0.7585 (t0)
REVERT: A  768 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6960 (pp20)
REVERT: A  793 GLN cc_start: 0.8127 (mt0) cc_final: 0.7786 (tt0)
REVERT: A  845 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7687 (mtmm)
REVERT: A  846 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7463 (mp10)
  outliers start: 35
  outliers final: 30
  residues processed: 276
  average time/residue: 0.3207
  time to fit residues: 119.9210
Evaluate side-chains
  284 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 251
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
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  584 LEU
Chi-restraints excluded: chain B residue  587 LEU
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  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  925 GLU
Chi-restraints excluded: chain B residue  965 LYS
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  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  431 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  539 PHE
Chi-restraints excluded: chain A residue  596 ASN
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  729 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 127 optimal weight:   10.0000
   chunk 32 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 112 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   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 614 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 402 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.180779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.148614 restraints weight = 26527.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 3.13
r_work: 0.3745 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3748 r_free = 0.3748    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3748 r_free = 0.3748    target_work(ls_wunit_k1) = 0.133         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.3144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10758  Z= 0.184
  Angle     :  0.636   7.208  14524  Z= 0.330
  Chirality :  0.045   0.301   1671
  Planarity :  0.004   0.036   1844
  Dihedral  :  8.532  82.412   1479
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 22.78 %
    Favored  : 73.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.23), residues: 1306
  helix:  0.64 (0.19), residues: 718
  sheet: -2.46 (0.40), residues: 140
  loop : -1.47 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 764 
 HIS   0.014   0.001   HIS B 614 
 PHE   0.039   0.002   PHE A 760 
 TYR   0.023   0.002   TYR A 815 
 ARG   0.011   0.001   ARG A 638 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03927 (  553)
  hydrogen bonds       : angle       4.41499 ( 1589)
  covalent geometry    : bond        0.00421 (10758)
  covalent geometry    : angle       0.63552 (14524)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7922.34 seconds
wall clock time: 144 minutes 28.99 seconds (8668.99 seconds total)