Starting phenix.real_space_refine
on Wed Sep 17 20:14:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6gkm_0024/09_2025/6gkm_0024.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6gkm_0024/09_2025/6gkm_0024.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6gkm_0024/09_2025/6gkm_0024.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6gkm_0024/09_2025/6gkm_0024.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6gkm_0024/09_2025/6gkm_0024.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6gkm_0024/09_2025/6gkm_0024.map"
  }
  resolution = 3.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.013
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      31      5.49       5
     S      35      5.16       5
     C    3778      2.51       5
     N    1072      2.21       5
     O    1243      1.98       5
     H    4402      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10562
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 689, 9933
          Classifications: {'peptide': 689}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 21, 'TRANS': 667}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 14
    Chain: "X"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 308
          Classifications: {'RNA': 14}
          Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 3}
          Link IDs: {'rna3p': 13}
    Chain: "Y"
      Number of atoms: 289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 289
          Classifications: {'RNA': 14}
          Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 11}
          Link IDs: {'rna3p': 13}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' ZN': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8383  SG  CYS A 907      77.644  31.514  37.882  1.00129.19           S
  ATOM   8430  SG  CYS A 910      80.696  31.296  37.972  1.00129.60           S
  ATOM   9100  SG  CYS A 962      79.571  31.817  41.539  1.00129.10           S
  ATOM   9119  SG  CYS A 964      79.466  34.419  39.261  1.00130.93           S

  Time building chain proxies: 2.01, per 1000 atoms: 0.19
  Number of scatterers: 10562
  At special positions: 0
  Unit cell: (101.65, 85.6, 68.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      35     16.00
     P      31     15.00
     O    1243      8.00
     N    1072      7.00
     C    3778      6.00
     H    4402      1.00
    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: 1.06
  Conformation dependent library (CDL) restraints added in 237.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1101 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 962 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 910 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 964 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 907 "
      Number of angles added : 6


  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1318

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 6 sheets defined
      52.2% alpha, 9.7% beta
      14 base pairs and 21 stacking pairs defined.
    Time for finding SS restraints: 1.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 310 through 318
      removed outlier: 3.573A  pdb=" N   GLU A 315 " --> pdb=" O   PRO A 311 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   VAL A 316 " --> pdb=" O   TYR A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 322
    Processing helix  chain 'A' and resid 335 through 354
    Processing helix  chain 'A' and resid 367 through 377
      removed outlier: 3.977A  pdb=" N   GLU A 371 " --> pdb=" O   VAL A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 383
    Processing helix  chain 'A' and resid 400 through 405
      removed outlier: 3.533A  pdb=" N   VAL A 405 " --> pdb=" O   PHE A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 428
      removed outlier: 3.656A  pdb=" N   GLU A 419 " --> pdb=" O   ALA A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 438
    Processing helix  chain 'A' and resid 445 through 449
    Processing helix  chain 'A' and resid 455 through 476
      removed outlier: 3.674A  pdb=" N   MET A 459 " --> pdb=" O   TYR A 455 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   LYS A 474 " --> pdb=" O   ASN A 470 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLN A 475 " --> pdb=" O   ASP A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 514
    Processing helix  chain 'A' and resid 525 through 533
      removed outlier: 3.931A  pdb=" N   LEU A 529 " --> pdb=" O   ASN A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 567
      removed outlier: 3.879A  pdb=" N   LYS A 552 " --> pdb=" O   GLU A 548 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ILE A 558 " --> pdb=" O   LYS A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 594
    Processing helix  chain 'A' and resid 598 through 616
      removed outlier: 3.688A  pdb=" N   LYS A 607 " --> pdb=" O   GLU A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 643
      removed outlier: 3.789A  pdb=" N   ALA A 623 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 682
      removed outlier: 3.584A  pdb=" N   GLU A 674 " --> pdb=" O   ASP A 670 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ASP A 682 " --> pdb=" O   ASN A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 692
      removed outlier: 3.619A  pdb=" N   GLU A 692 " --> pdb=" O   LYS A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 693 through 697
      removed outlier: 4.120A  pdb=" N   GLU A 697 " --> pdb=" O   PRO A 694 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 715
      removed outlier: 4.021A  pdb=" N   ILE A 702 " --> pdb=" O   ASN A 698 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLN A 711 " --> pdb=" O   THR A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 741
    Processing helix  chain 'A' and resid 741 through 747
      removed outlier: 3.985A  pdb=" N   ALA A 745 " --> pdb=" O   ASN A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 767 through 781
    Processing helix  chain 'A' and resid 812 through 821
    Processing helix  chain 'A' and resid 840 through 863
      removed outlier: 3.797A  pdb=" N   TYR A 855 " --> pdb=" O   GLU A 851 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   LYS A 856 " --> pdb=" O   LYS A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 893
      removed outlier: 3.548A  pdb=" N   LYS A 885 " --> pdb=" O   ILE A 881 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   LYS A 887 " --> pdb=" O   GLU A 883 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ARG A 890 " --> pdb=" O   MET A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 932 through 937
    Processing sheet with id=AA1, first strand: chain 'A' and resid 326 through 329
      removed outlier: 6.418A  pdb=" N   ILE A 326 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 8.207A  pdb=" N   THR A 489 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   ILE A 328 " --> pdb=" O   THR A 489 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   ILE A 361 " --> pdb=" O   ILE A 442 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   VAL A 360 " --> pdb=" O   ILE A 411 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   SER A 413 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   VAL A 362 " --> pdb=" O   SER A 413 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 543
      removed outlier: 3.672A  pdb=" N   THR A 834 " --> pdb=" O   VAL A 541 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 721 through 724
      removed outlier: 6.595A  pdb=" N   HIS A 752 " --> pdb=" O   ILE A 787 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 912 through 916
      removed outlier: 4.053A  pdb=" N   MET A 912 " --> pdb=" O   CYS A 907 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   LEU A 905 " --> pdb=" O   VAL A 914 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   SER A 916 " --> pdb=" O   ILE A 903 " (cutoff:3.500A)
      removed outlier: 7.426A  pdb=" N   ILE A 903 " --> pdb=" O   SER A 916 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 920 through 923
    Processing sheet with id=AA6, first strand: chain 'A' and resid 940 through 941
      removed outlier: 4.219A  pdb=" N   GLY A 969 " --> pdb=" O   ILE A 960 " (cutoff:3.500A)

    260 hydrogen bonds defined for protein.
    756 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      37 hydrogen bonds
      74 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      21 stacking parallelities
  Total time for adding SS restraints: 2.27

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4391
        1.03 -     1.23: 18
        1.23 -     1.42: 2607
        1.42 -     1.62: 3646
        1.62 -     1.81: 56
  Bond restraints: 10718
  Sorted by residual:
  bond pdb=" C4  ATP A1102 "
       pdb=" C5  ATP A1102 "
    ideal  model  delta    sigma   weight residual
    1.388  1.462 -0.074 1.00e-02 1.00e+04 5.52e+01
  bond pdb=" C5  ATP A1102 "
       pdb=" C6  ATP A1102 "
    ideal  model  delta    sigma   weight residual
    1.409  1.476 -0.067 1.00e-02 1.00e+04 4.49e+01
  bond pdb=" C8  ATP A1102 "
       pdb=" N7  ATP A1102 "
    ideal  model  delta    sigma   weight residual
    1.310  1.358 -0.048 1.00e-02 1.00e+04 2.32e+01
  bond pdb=" C4  ATP A1102 "
       pdb=" N9  ATP A1102 "
    ideal  model  delta    sigma   weight residual
    1.374  1.327  0.047 1.00e-02 1.00e+04 2.17e+01
  bond pdb=" C5  ATP A1102 "
       pdb=" N7  ATP A1102 "
    ideal  model  delta    sigma   weight residual
    1.387  1.345  0.042 1.00e-02 1.00e+04 1.76e+01
  ... (remaining 10713 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.84: 18681
       10.84 -    21.69: 8
       21.69 -    32.53: 0
       32.53 -    43.38: 0
       43.38 -    54.22: 14
  Bond angle restraints: 18703
  Sorted by residual:
  angle pdb=" PB  ATP A1102 "
        pdb=" O3B ATP A1102 "
        pdb=" PG  ATP A1102 "
      ideal   model   delta    sigma   weight residual
     139.87  120.71   19.16 1.00e+00 1.00e+00 3.67e+02
  angle pdb=" C   LYS A 884 "
        pdb=" N   LYS A 885 "
        pdb=" H   LYS A 885 "
      ideal   model   delta    sigma   weight residual
     124.88   70.66   54.22 3.00e+00 1.11e-01 3.27e+02
  angle pdb=" CA  VAL A 888 "
        pdb=" N   VAL A 888 "
        pdb=" H   VAL A 888 "
      ideal   model   delta    sigma   weight residual
     114.62   60.44   54.18 3.00e+00 1.11e-01 3.26e+02
  angle pdb=" C   LYS A 887 "
        pdb=" N   VAL A 888 "
        pdb=" H   VAL A 888 "
      ideal   model   delta    sigma   weight residual
     124.92   70.76   54.16 3.00e+00 1.11e-01 3.26e+02
  angle pdb=" C   MET A 886 "
        pdb=" N   LYS A 887 "
        pdb=" H   LYS A 887 "
      ideal   model   delta    sigma   weight residual
     125.01   71.07   53.94 3.00e+00 1.11e-01 3.23e+02
  ... (remaining 18698 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.35: 4886
       16.35 -    32.69: 398
       32.69 -    49.04: 75
       49.04 -    65.39: 55
       65.39 -    81.74: 18
  Dihedral angle restraints: 5432
    sinusoidal: 3145
      harmonic: 2287
  Sorted by residual:
  dihedral pdb=" CA  SER A 413 "
           pdb=" C   SER A 413 "
           pdb=" N   THR A 414 "
           pdb=" CA  THR A 414 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.05   29.95     0      5.00e+00 4.00e-02 3.59e+01
  dihedral pdb=" CA  ASN A 802 "
           pdb=" C   ASN A 802 "
           pdb=" N   ILE A 803 "
           pdb=" CA  ILE A 803 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.89  -25.11     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  SER A 995 "
           pdb=" C   SER A 995 "
           pdb=" N   PRO A 996 "
           pdb=" CA  PRO A 996 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.90   24.10     0      5.00e+00 4.00e-02 2.32e+01
  ... (remaining 5429 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 664
       0.038 -    0.075: 225
       0.075 -    0.113: 79
       0.113 -    0.150: 24
       0.150 -    0.188: 3
  Chirality restraints: 995
  Sorted by residual:
  chirality pdb=" CB  ILE A 803 "
            pdb=" CA  ILE A 803 "
            pdb=" CG1 ILE A 803 "
            pdb=" CG2 ILE A 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.80e-01
  chirality pdb=" CB  ILE A 458 "
            pdb=" CA  ILE A 458 "
            pdb=" CG1 ILE A 458 "
            pdb=" CG2 ILE A 458 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.47e-01
  chirality pdb=" CA  ILE A 480 "
            pdb=" N   ILE A 480 "
            pdb=" C   ILE A 480 "
            pdb=" CB  ILE A 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.42e-01
  ... (remaining 992 not shown)

  Planarity restraints: 1576
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 995 "   -0.024 5.00e-02 4.00e+02   3.59e-02 2.06e+00
        pdb=" N   PRO A 996 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 996 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 996 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 724 "   -0.017 2.00e-02 2.50e+03   8.17e-03 2.00e+00
        pdb=" CG  PHE A 724 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 724 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 724 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 724 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 724 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 724 "   -0.006 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 724 "    0.001 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 724 "    0.003 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 724 "   -0.005 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 724 "   -0.003 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 724 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 330 "   -0.023 5.00e-02 4.00e+02   3.49e-02 1.95e+00
        pdb=" N   PRO A 331 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 331 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 331 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1573 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 487
        2.19 -     2.80: 18970
        2.80 -     3.40: 24829
        3.40 -     4.00: 33489
        4.00 -     4.60: 52485
  Nonbonded interactions: 130260
  Sorted by model distance:
  nonbonded pdb=" H   LYS A 498 "
            pdb=" HA  LYS A 498 "
     model   vdw
     1.594 1.816
  nonbonded pdb=" H   VAL A 888 "
            pdb=" HA  VAL A 888 "
     model   vdw
     1.611 1.816
  nonbonded pdb=" H   LYS A 887 "
            pdb=" HA  LYS A 887 "
     model   vdw
     1.623 1.816
  nonbonded pdb=" H   GLU A 794 "
            pdb=" HA  GLU A 794 "
     model   vdw
     1.644 1.816
  nonbonded pdb="HH21 ARG A 728 "
            pdb=" OP2   U Y   7 "
     model   vdw
     1.653 2.450
  ... (remaining 130255 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.740
  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:             0.070
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.990
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
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      :  0.008   0.109   6320  Z= 0.370
  Angle     :  1.057  25.679   8640  Z= 0.620
  Chirality :  0.046   0.188    995
  Planarity :  0.004   0.036    991
  Dihedral  : 13.926  81.736   2654
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.69 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.24 %
    Favored  : 96.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.66 (0.27), residues: 681
  helix: -1.11 (0.25), residues: 335
  sheet: -3.19 (0.46), residues: 87
  loop : -3.90 (0.31), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 619 
 TYR   0.020   0.002   TYR A 342 
 PHE   0.021   0.003   PHE A 724 
 TRP   0.012   0.002   TRP A 737 
 HIS   0.012   0.003   HIS A 506 

Details of bonding type rmsd
  covalent geometry    : bond        0.00736 ( 6316)
  covalent geometry    : angle       0.98168 ( 8634)
  hydrogen bonds       : bond        0.14199 (  297)
  hydrogen bonds       : angle       5.85984 (  830)
  metal coordination   : bond        0.08797 (    4)
  metal coordination   : angle      14.93511 (    6)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  181 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  580 GLU cc_start: 0.8552 (tt0) cc_final: 0.8198 (tm-30)
REVERT: A  882 LEU cc_start: 0.9281 (mp) cc_final: 0.8923 (mp)
REVERT: A  884 LYS cc_start: 0.9113 (tptp) cc_final: 0.8862 (tptp)
REVERT: A  935 PHE cc_start: 0.8628 (t80) cc_final: 0.8398 (t80)
REVERT: A  979 LEU cc_start: 0.8029 (pt) cc_final: 0.7617 (pt)
  outliers start: 1
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2153
  time to fit residues: 47.6889
Evaluate side-chains
  86 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    9.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 457 ASN
A 595 ASN
A 784 ASN
A 986 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.095519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.075987 restraints weight = 35487.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.080131 restraints weight = 14539.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.082851 restraints weight = 8426.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.084618 restraints weight = 5877.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.085658 restraints weight = 4593.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6320  Z= 0.144
  Angle     :  0.719  21.068   8640  Z= 0.392
  Chirality :  0.038   0.153    995
  Planarity :  0.004   0.039    991
  Dihedral  : 15.956  86.902   1209
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 16.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 12.16 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.21 (0.31), residues: 681
  helix:  0.35 (0.28), residues: 342
  sheet: -2.82 (0.47), residues: 84
  loop : -3.60 (0.31), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 375 
 TYR   0.019   0.001   TYR A 342 
 PHE   0.008   0.001   PHE A 680 
 TRP   0.005   0.001   TRP A 582 
 HIS   0.007   0.001   HIS A 928 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 6316)
  covalent geometry    : angle       0.70553 ( 8634)
  hydrogen bonds       : bond        0.04135 (  297)
  hydrogen bonds       : angle       4.40851 (  830)
  metal coordination   : bond        0.00815 (    4)
  metal coordination   : angle       5.23218 (    6)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  99 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  580 GLU cc_start: 0.8606 (tt0) cc_final: 0.8099 (tm-30)
REVERT: A  588 LYS cc_start: 0.9212 (mtpt) cc_final: 0.8826 (mttp)
REVERT: A  610 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8751 (tm-30)
  outliers start: 8
  outliers final: 7
  residues processed: 97
  average time/residue: 0.1729
  time to fit residues: 21.5950
Evaluate side-chains
  89 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  595 ASN
Chi-restraints excluded: chain A residue  619 ARG
Chi-restraints excluded: chain A residue  766 MET
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  834 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 69 optimal weight:   10.0000
   chunk 30 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.092574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.072887 restraints weight = 36012.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.076936 restraints weight = 14588.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.079612 restraints weight = 8450.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.081350 restraints weight = 5915.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.082478 restraints weight = 4642.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.3616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6320  Z= 0.160
  Angle     :  0.688  20.979   8640  Z= 0.380
  Chirality :  0.038   0.205    995
  Planarity :  0.003   0.038    991
  Dihedral  : 15.713  89.958   1209
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 17.47
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.08 %
    Favored  : 91.78 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 13.94 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.47 (0.32), residues: 681
  helix:  1.03 (0.29), residues: 344
  sheet: -2.47 (0.50), residues: 84
  loop : -3.40 (0.32), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 547 
 TYR   0.015   0.001   TYR A 342 
 PHE   0.008   0.001   PHE A 401 
 TRP   0.004   0.001   TRP A 737 
 HIS   0.008   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6316)
  covalent geometry    : angle       0.68107 ( 8634)
  hydrogen bonds       : bond        0.03685 (  297)
  hydrogen bonds       : angle       4.14342 (  830)
  metal coordination   : bond        0.00751 (    4)
  metal coordination   : angle       3.87768 (    6)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  87 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  531 HIS cc_start: 0.8364 (m-70) cc_final: 0.8099 (m-70)
REVERT: A  580 GLU cc_start: 0.8699 (tt0) cc_final: 0.8199 (tm-30)
REVERT: A  588 LYS cc_start: 0.9299 (mtpt) cc_final: 0.8900 (mttp)
REVERT: A  970 THR cc_start: 0.9365 (p) cc_final: 0.9106 (p)
  outliers start: 7
  outliers final: 5
  residues processed: 86
  average time/residue: 0.1851
  time to fit residues: 20.5723
Evaluate side-chains
  76 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  619 ARG
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  785 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 33 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0870
   chunk 14 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    2.2164

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

Flipped N/Q/H residues before XYZ refinement:
A 531 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.091657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.071940 restraints weight = 35719.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.075920 restraints weight = 14436.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.078542 restraints weight = 8378.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.080260 restraints weight = 5892.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.081371 restraints weight = 4664.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6320  Z= 0.156
  Angle     :  0.684  21.038   8640  Z= 0.376
  Chirality :  0.037   0.145    995
  Planarity :  0.003   0.037    991
  Dihedral  : 15.605  83.589   1209
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 17.47
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.52 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 13.94 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.33), residues: 681
  helix:  1.47 (0.29), residues: 344
  sheet: -2.21 (0.50), residues: 86
  loop : -3.26 (0.32), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 890 
 TYR   0.012   0.001   TYR A 455 
 PHE   0.009   0.001   PHE A 401 
 TRP   0.005   0.001   TRP A 737 
 HIS   0.007   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 6316)
  covalent geometry    : angle       0.67959 ( 8634)
  hydrogen bonds       : bond        0.03459 (  297)
  hydrogen bonds       : angle       3.95303 (  830)
  metal coordination   : bond        0.00685 (    4)
  metal coordination   : angle       3.13543 (    6)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  89 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  371 GLU cc_start: 0.8438 (tt0) cc_final: 0.8212 (tt0)
REVERT: A  419 GLU cc_start: 0.8524 (tp30) cc_final: 0.8295 (tp30)
REVERT: A  580 GLU cc_start: 0.8793 (tt0) cc_final: 0.8335 (tm-30)
REVERT: A  970 THR cc_start: 0.9343 (p) cc_final: 0.9119 (p)
  outliers start: 10
  outliers final: 10
  residues processed: 86
  average time/residue: 0.1668
  time to fit residues: 18.9671
Evaluate side-chains
  80 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  619 ARG
Chi-restraints excluded: chain A residue  628 GLU
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  834 THR
Chi-restraints excluded: chain A residue  972 MET
Chi-restraints excluded: chain A residue  979 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 56 optimal weight:   10.0000
   chunk 12 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 46 optimal weight:    7.9990
   overall best weight:    2.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.090119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.070783 restraints weight = 35491.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.074666 restraints weight = 14329.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.077236 restraints weight = 8281.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.078911 restraints weight = 5844.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.079990 restraints weight = 4613.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.4625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6320  Z= 0.152
  Angle     :  0.671  21.037   8640  Z= 0.370
  Chirality :  0.037   0.147    995
  Planarity :  0.003   0.035    991
  Dihedral  : 14.850  74.092   1209
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 17.64
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.78 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.94 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.70 (0.33), residues: 681
  helix:  1.66 (0.29), residues: 344
  sheet: -1.38 (0.56), residues: 74
  loop : -3.28 (0.32), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 599 
 TYR   0.011   0.001   TYR A 455 
 PHE   0.010   0.001   PHE A 401 
 TRP   0.004   0.001   TRP A 737 
 HIS   0.008   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 6316)
  covalent geometry    : angle       0.66736 ( 8634)
  hydrogen bonds       : bond        0.03367 (  297)
  hydrogen bonds       : angle       3.83892 (  830)
  metal coordination   : bond        0.00634 (    4)
  metal coordination   : angle       2.80658 (    6)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  84 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.341 
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: A  371 GLU cc_start: 0.8604 (tt0) cc_final: 0.8394 (tt0)
REVERT: A  580 GLU cc_start: 0.8868 (tt0) cc_final: 0.8377 (tm-30)
REVERT: A  827 GLU cc_start: 0.6540 (mm-30) cc_final: 0.6048 (mm-30)
  outliers start: 12
  outliers final: 11
  residues processed: 81
  average time/residue: 0.1487
  time to fit residues: 16.4639
Evaluate side-chains
  77 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  619 ARG
Chi-restraints excluded: chain A residue  628 GLU
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  785 LEU
Chi-restraints excluded: chain A residue  853 MET
Chi-restraints excluded: chain A residue  956 THR
Chi-restraints excluded: chain A residue  972 MET
Chi-restraints excluded: chain A residue  979 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 68 optimal weight:    9.9990
   chunk 66 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 10 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0010
   chunk 46 optimal weight:    4.9990
   overall best weight:    2.3992

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

Flipped N/Q/H residues before XYZ refinement:
** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.089005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.070140 restraints weight = 36526.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.073955 restraints weight = 14987.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2987 r_free = 0.2987 target = 0.076471 restraints weight = 8728.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.078110 restraints weight = 6157.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.079061 restraints weight = 4873.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.4986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6320  Z= 0.163
  Angle     :  0.680  21.025   8640  Z= 0.373
  Chirality :  0.038   0.146    995
  Planarity :  0.003   0.034    991
  Dihedral  : 14.677  74.231   1209
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 15.07 %
    Favored  : 83.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.33), residues: 681
  helix:  1.80 (0.29), residues: 344
  sheet: -1.54 (0.59), residues: 66
  loop : -3.21 (0.31), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1009 
 TYR   0.011   0.001   TYR A 455 
 PHE   0.011   0.001   PHE A 401 
 TRP   0.003   0.001   TRP A 737 
 HIS   0.022   0.002   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6316)
  covalent geometry    : angle       0.67657 ( 8634)
  hydrogen bonds       : bond        0.03380 (  297)
  hydrogen bonds       : angle       3.85559 (  830)
  metal coordination   : bond        0.00645 (    4)
  metal coordination   : angle       2.79231 (    6)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  77 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  400 SER cc_start: 0.8464 (m) cc_final: 0.8159 (p)
REVERT: A  463 LEU cc_start: 0.9455 (mt) cc_final: 0.9161 (mt)
REVERT: A  580 GLU cc_start: 0.8877 (tt0) cc_final: 0.8475 (tm-30)
  outliers start: 8
  outliers final: 8
  residues processed: 74
  average time/residue: 0.1276
  time to fit residues: 13.5330
Evaluate side-chains
  70 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  619 ARG
Chi-restraints excluded: chain A residue  628 GLU
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  853 MET
Chi-restraints excluded: chain A residue  972 MET
Chi-restraints excluded: chain A residue  979 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 51 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0970
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.091241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.072085 restraints weight = 35217.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.076057 restraints weight = 14118.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.078707 restraints weight = 8143.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.080413 restraints weight = 5664.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.081464 restraints weight = 4436.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.5116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   6320  Z= 0.090
  Angle     :  0.651  21.247   8640  Z= 0.357
  Chirality :  0.037   0.149    995
  Planarity :  0.003   0.035    991
  Dihedral  : 14.636  73.773   1209
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 17.14
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  6.90 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 15.40 %
    Favored  : 83.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.33), residues: 681
  helix:  2.11 (0.29), residues: 341
  sheet: -1.67 (0.57), residues: 70
  loop : -2.97 (0.33), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 843 
 TYR   0.007   0.001   TYR A 455 
 PHE   0.010   0.001   PHE A 401 
 TRP   0.004   0.001   TRP A 737 
 HIS   0.006   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 ( 6316)
  covalent geometry    : angle       0.64832 ( 8634)
  hydrogen bonds       : bond        0.03026 (  297)
  hydrogen bonds       : angle       3.56594 (  830)
  metal coordination   : bond        0.00359 (    4)
  metal coordination   : angle       2.27154 (    6)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  80 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.361 
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: A  388 ILE cc_start: 0.8977 (mp) cc_final: 0.8634 (tt)
REVERT: A  400 SER cc_start: 0.8461 (m) cc_final: 0.8116 (p)
REVERT: A  463 LEU cc_start: 0.9379 (mt) cc_final: 0.9028 (mt)
REVERT: A  580 GLU cc_start: 0.8923 (tt0) cc_final: 0.8589 (tm-30)
  outliers start: 8
  outliers final: 5
  residues processed: 77
  average time/residue: 0.1031
  time to fit residues: 11.8214
Evaluate side-chains
  72 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  628 GLU
Chi-restraints excluded: chain A residue  853 MET
Chi-restraints excluded: chain A residue  972 MET
Chi-restraints excluded: chain A residue  979 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 34 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.088083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.069053 restraints weight = 36523.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.072814 restraints weight = 15212.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.075273 restraints weight = 8944.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.076879 restraints weight = 6372.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.077909 restraints weight = 5081.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.5400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6320  Z= 0.213
  Angle     :  0.711  20.922   8640  Z= 0.389
  Chirality :  0.038   0.145    995
  Planarity :  0.003   0.030    991
  Dihedral  : 14.713  74.772   1209
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 19.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.96 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.88 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.33), residues: 681
  helix:  1.83 (0.29), residues: 350
  sheet: -1.86 (0.55), residues: 73
  loop : -3.19 (0.33), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 461 
 TYR   0.014   0.001   TYR A 455 
 PHE   0.013   0.001   PHE A 401 
 TRP   0.004   0.001   TRP A 582 
 HIS   0.005   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 6316)
  covalent geometry    : angle       0.70676 ( 8634)
  hydrogen bonds       : bond        0.03582 (  297)
  hydrogen bonds       : angle       3.98474 (  830)
  metal coordination   : bond        0.00835 (    4)
  metal coordination   : angle       3.08412 (    6)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  73 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.7878 (t70)
REVERT: A  400 SER cc_start: 0.8617 (m) cc_final: 0.8249 (p)
REVERT: A  463 LEU cc_start: 0.9462 (mt) cc_final: 0.9189 (mt)
REVERT: A  580 GLU cc_start: 0.8942 (tt0) cc_final: 0.8575 (tm-30)
  outliers start: 10
  outliers final: 9
  residues processed: 70
  average time/residue: 0.1213
  time to fit residues: 12.3276
Evaluate side-chains
  73 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 ASP
Chi-restraints excluded: chain A residue  427 SER
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  619 ARG
Chi-restraints excluded: chain A residue  628 GLU
Chi-restraints excluded: chain A residue  780 THR
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  853 MET
Chi-restraints excluded: chain A residue  972 MET
Chi-restraints excluded: chain A residue  979 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 68 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.089491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.070583 restraints weight = 36032.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.074494 restraints weight = 14982.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.077037 restraints weight = 8728.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.078545 restraints weight = 6151.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.079719 restraints weight = 4948.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.5463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6320  Z= 0.114
  Angle     :  0.663  21.143   8640  Z= 0.363
  Chirality :  0.037   0.148    995
  Planarity :  0.003   0.031    991
  Dihedral  : 14.540  74.220   1209
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 18.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.21 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.33), residues: 681
  helix:  1.95 (0.29), residues: 350
  sheet: -1.66 (0.56), residues: 73
  loop : -3.08 (0.33), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 843 
 TYR   0.009   0.001   TYR A 455 
 PHE   0.011   0.001   PHE A 401 
 TRP   0.004   0.001   TRP A 737 
 HIS   0.005   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 6316)
  covalent geometry    : angle       0.66027 ( 8634)
  hydrogen bonds       : bond        0.03169 (  297)
  hydrogen bonds       : angle       3.72830 (  830)
  metal coordination   : bond        0.00439 (    4)
  metal coordination   : angle       2.35451 (    6)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  388 ILE cc_start: 0.8993 (mp) cc_final: 0.8644 (tt)
REVERT: A  394 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7815 (t70)
REVERT: A  400 SER cc_start: 0.8486 (m) cc_final: 0.8126 (p)
REVERT: A  463 LEU cc_start: 0.9395 (mt) cc_final: 0.9114 (mt)
  outliers start: 8
  outliers final: 7
  residues processed: 72
  average time/residue: 0.1107
  time to fit residues: 12.0096
Evaluate side-chains
  74 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 ASP
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  628 GLU
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  853 MET
Chi-restraints excluded: chain A residue  972 MET
Chi-restraints excluded: chain A residue  979 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 2 optimal weight:    0.4980
   chunk 28 optimal weight:    6.9990
   chunk 69 optimal weight:   10.0000
   chunk 9 optimal weight:    0.6980
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 59 optimal weight:    6.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.090268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.071100 restraints weight = 35655.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.075075 restraints weight = 14454.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.077729 restraints weight = 8306.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.079407 restraints weight = 5777.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.080450 restraints weight = 4531.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.5577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6320  Z= 0.099
  Angle     :  0.654  21.072   8640  Z= 0.359
  Chirality :  0.037   0.148    995
  Planarity :  0.003   0.034    991
  Dihedral  : 14.486  74.024   1209
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 17.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.69 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.34), residues: 681
  helix:  2.12 (0.29), residues: 350
  sheet: -1.49 (0.57), residues: 73
  loop : -2.98 (0.34), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 619 
 TYR   0.009   0.001   TYR A 455 
 PHE   0.010   0.001   PHE A 401 
 TRP   0.004   0.001   TRP A 737 
 HIS   0.004   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 6316)
  covalent geometry    : angle       0.65177 ( 8634)
  hydrogen bonds       : bond        0.03038 (  297)
  hydrogen bonds       : angle       3.62966 (  830)
  metal coordination   : bond        0.00396 (    4)
  metal coordination   : angle       2.31724 (    6)

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

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

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1362 Ramachandran restraints generated.
    681 Oldfield, 0 Emsley, 681 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue LEU  669 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  743 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue SER  838 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue SER  880 is missing expected H atoms. Skipping.
Residue ILE  881 is missing expected H atoms. Skipping.
Residue LEU  882 is missing expected H atoms. Skipping.
Residue LYS  884 is missing expected H atoms. Skipping.
Residue LYS  885 is missing expected H atoms. Skipping.
Residue MET  886 is missing expected H atoms. Skipping.
Residue LYS  887 is missing expected H atoms. Skipping.
Residue VAL  888 is missing expected H atoms. Skipping.
Residue LYS  889 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  77 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7892 (t70)
REVERT: A  400 SER cc_start: 0.8494 (m) cc_final: 0.8125 (p)
REVERT: A  463 LEU cc_start: 0.9369 (mt) cc_final: 0.9105 (mt)
REVERT: A  580 GLU cc_start: 0.8894 (tt0) cc_final: 0.8222 (tm-30)
REVERT: A  678 ASN cc_start: 0.8448 (m110) cc_final: 0.8027 (p0)
  outliers start: 8
  outliers final: 7
  residues processed: 74
  average time/residue: 0.1018
  time to fit residues: 11.6002
Evaluate side-chains
  75 residues out of total 619 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 ASP
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain A residue  628 GLU
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  796 LEU
Chi-restraints excluded: chain A residue  853 MET
Chi-restraints excluded: chain A residue  972 MET
Chi-restraints excluded: chain A residue  979 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 24 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 563 GLN
** A 974 HIS ** 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 = 0.3222 r_free = 0.3222 target = 0.089532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.070513 restraints weight = 36066.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.074386 restraints weight = 15097.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.076929 restraints weight = 8830.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.078571 restraints weight = 6230.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.079649 restraints weight = 4923.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.5715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6320  Z= 0.125
  Angle     :  0.664  21.123   8640  Z= 0.364
  Chirality :  0.037   0.148    995
  Planarity :  0.003   0.031    991
  Dihedral  : 14.467  74.382   1209
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 18.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.69 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.12 (0.34), residues: 681
  helix:  2.10 (0.29), residues: 350
  sheet: -1.77 (0.51), residues: 89
  loop : -2.85 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 619 
 TYR   0.010   0.001   TYR A 455 
 PHE   0.012   0.001   PHE A 401 
 TRP   0.003   0.001   TRP A 582 
 HIS   0.004   0.001   HIS A 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 6316)
  covalent geometry    : angle       0.66170 ( 8634)
  hydrogen bonds       : bond        0.03087 (  297)
  hydrogen bonds       : angle       3.69620 (  830)
  metal coordination   : bond        0.00483 (    4)
  metal coordination   : angle       2.38959 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1866.10 seconds
wall clock time: 32 minutes 43.11 seconds (1963.11 seconds total)