Starting phenix.real_space_refine
on Fri Jan 17 00:02:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5d_44208/01_2025/9b5d_44208.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5d_44208/01_2025/9b5d_44208.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5d_44208/01_2025/9b5d_44208.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5d_44208/01_2025/9b5d_44208.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5d_44208/01_2025/9b5d_44208.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5d_44208/01_2025/9b5d_44208.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.071
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      2      5.21       5
     S      43      5.16       5
     C    6449      2.51       5
     N    1678      2.21       5
     O    1953      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 10128
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 985, 7734
          Classifications: {'peptide': 985}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 601
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "C"
      Number of atoms: 1158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1158
          Classifications: {'peptide': 147}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131}
    Chain: "D"
      Number of atoms: 596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 596
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ATP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'A1AIV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.58, per 1000 atoms: 0.65
  Number of scatterers: 10128
  At special positions: 0
  Unit cell: (100.016, 98.952, 119.168, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      43     16.00
     P       3     15.00
     Mg      2     11.99
     O    1953      8.00
     N    1678      7.00
     C    6449      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 593 " - pdb=" SG  CYS C  85 " distance=2.91

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.48
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2404

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 11 sheets defined
      45.9% alpha, 16.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.750A  pdb=" N   TYR A  25 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 36
    Processing helix  chain 'A' and resid 46 through 60
    Processing helix  chain 'A' and resid 73 through 79
      removed outlier: 3.681A  pdb=" N   SER A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 4.014A  pdb=" N   ILE A  88 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
      removed outlier: 4.326A  pdb=" N   SER A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   LYS A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 123
      removed outlier: 3.607A  pdb=" N   ASN A 122 " --> pdb=" O   TYR A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 146
      removed outlier: 3.711A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   LYS A 145 " --> pdb=" O   ASP A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 223
      removed outlier: 3.691A  pdb=" N   ASP A 223 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 4.291A  pdb=" N   LYS A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ASP A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 305
      removed outlier: 3.652A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN A 296 " --> pdb=" O   HIS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 332
    Processing helix  chain 'A' and resid 339 through 349
    Processing helix  chain 'A' and resid 354 through 375
    Processing helix  chain 'A' and resid 389 through 392
    Processing helix  chain 'A' and resid 410 through 418
      removed outlier: 4.406A  pdb=" N   VAL A 416 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 427
      removed outlier: 3.555A  pdb=" N   SER A 427 " --> pdb=" O   GLU A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 450
    Processing helix  chain 'A' and resid 468 through 474
      removed outlier: 3.619A  pdb=" N   ASN A 473 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 483
    Processing helix  chain 'A' and resid 486 through 499
    Processing helix  chain 'A' and resid 500 through 503
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 3.847A  pdb=" N   GLU A 518 " --> pdb=" O   PRO A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 528
      removed outlier: 3.839A  pdb=" N   LYS A 528 " --> pdb=" O   GLU A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 553
      removed outlier: 3.568A  pdb=" N   ARG A 542 " --> pdb=" O   ASN A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 582
      removed outlier: 3.538A  pdb=" N   SER A 581 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   SER A 582 " --> pdb=" O   TYR A 579 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 578 through 582'
    Processing helix  chain 'A' and resid 591 through 597
    Processing helix  chain 'A' and resid 601 through 618
    Processing helix  chain 'A' and resid 618 through 628
    Processing helix  chain 'A' and resid 632 through 641
      removed outlier: 3.674A  pdb=" N   LYS A 639 " --> pdb=" O   GLU A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 656
    Processing helix  chain 'A' and resid 662 through 679
      removed outlier: 3.564A  pdb=" N   CYS A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 689
    Processing helix  chain 'A' and resid 718 through 737
    Processing helix  chain 'A' and resid 743 through 753
      removed outlier: 3.982A  pdb=" N   TYR A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLY A 753 " --> pdb=" O   ARG A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 794
      removed outlier: 4.015A  pdb=" N   GLN A 785 " --> pdb=" O   ASN A 781 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A 794 " --> pdb=" O   ILE A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 834
    Processing helix  chain 'A' and resid 840 through 849
    Processing helix  chain 'A' and resid 855 through 876
      removed outlier: 3.521A  pdb=" N   THR A 859 " --> pdb=" O   MET A 855 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LYS A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 883
      removed outlier: 3.691A  pdb=" N   GLU A 882 " --> pdb=" O   LYS A 879 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TYR A 883 " --> pdb=" O   ILE A 880 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 879 through 883'
    Processing helix  chain 'A' and resid 926 through 937
    Processing helix  chain 'A' and resid 958 through 966
    Processing helix  chain 'A' and resid 969 through 979
    Processing helix  chain 'B' and resid 22 through 35
    Processing helix  chain 'B' and resid 37 through 41
    Processing helix  chain 'B' and resid 55 through 60
    Processing helix  chain 'C' and resid 3 through 16
    Processing helix  chain 'C' and resid 86 through 90
    Processing helix  chain 'C' and resid 98 through 112
    Processing helix  chain 'C' and resid 120 through 130
    Processing helix  chain 'C' and resid 130 through 145
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 37 through 39
      No H-bonds generated for 'chain 'D' and resid 37 through 39'
    Processing helix  chain 'D' and resid 56 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111
      removed outlier: 6.806A  pdb=" N   VAL A  64 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ASN A  39 " --> pdb=" O   CYS A 125 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   VAL A 127 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   LEU A  41 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 8.255A  pdb=" N   SER A 155 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   TYR A 385 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172
    Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228
      removed outlier: 4.242A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   THR A 195 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   ILE A 188 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   VAL A 193 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228
      removed outlier: 4.242A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509
      removed outlier: 6.447A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   TYR A 509 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 6.440A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 509 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   SER A 559 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908
    Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922
      removed outlier: 6.352A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   VAL A 990 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
      removed outlier: 5.148A  pdb=" N   SER A 947 " --> pdb=" O   VAL A 990 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   GLU A 992 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   LEU A 945 " --> pdb=" O   GLU A 992 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   CYS A 994 " --> pdb=" O   THR A 943 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   SER A 947 " --> pdb=" O   LEU A 951 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   LEU A 951 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 922
      removed outlier: 6.352A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   CYS A 995 " --> pdb=" O   VAL A1003 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 12 through 16
      removed outlier: 3.889A  pdb=" N   ARG B  42 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 26
      removed outlier: 3.631A  pdb=" N   GLY C  24 " --> pdb=" O   GLN C  34 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   HIS C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 16

    487 hydrogen bonds defined for protein.
    1323 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.83

  Time building geometry restraints manager: 2.90 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1723
        1.27 -     1.40: 2410
        1.40 -     1.54: 6015
        1.54 -     1.67: 130
        1.67 -     1.81: 66
  Bond restraints: 10344
  Sorted by residual:
  bond pdb=" C04 A1AIV D 101 "
       pdb=" C05 A1AIV D 101 "
    ideal  model  delta    sigma   weight residual
    1.453  1.525 -0.072 2.00e-02 2.50e+03 1.30e+01
  bond pdb=" N   MET D   1 "
       pdb=" CA  MET D   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.92e+00
  bond pdb=" N   MET B   1 "
       pdb=" CA  MET B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.78e+00
  bond pdb=" C1' ATP A1103 "
       pdb=" C2' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.531  1.518  0.013 1.20e-02 6.94e+03 1.17e+00
  bond pdb=" C05 A1AIV D 101 "
       pdb=" N06 A1AIV D 101 "
    ideal  model  delta    sigma   weight residual
    1.151  1.132  0.019 2.00e-02 2.50e+03 9.05e-01
  ... (remaining 10339 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 13908
        1.90 -     3.79: 88
        3.79 -     5.69: 8
        5.69 -     7.58: 4
        7.58 -     9.48: 1
  Bond angle restraints: 14009
  Sorted by residual:
  angle pdb=" C   LYS A 381 "
        pdb=" N   GLN A 382 "
        pdb=" CA  GLN A 382 "
      ideal   model   delta    sigma   weight residual
     121.70  128.14   -6.44 1.80e+00 3.09e-01 1.28e+01
  angle pdb=" C03 A1AIV D 101 "
        pdb=" C02 A1AIV D 101 "
        pdb=" N01 A1AIV D 101 "
      ideal   model   delta    sigma   weight residual
     111.06  101.58    9.48 3.00e+00 1.11e-01 9.98e+00
  angle pdb=" C2' ATP A1103 "
        pdb=" C1' ATP A1103 "
        pdb=" O4' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     106.53  103.30    3.23 1.18e+00 7.24e-01 7.56e+00
  angle pdb=" C2' ATP A1103 "
        pdb=" C3' ATP A1103 "
        pdb=" O3' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.83  104.51    7.32 2.67e+00 1.40e-01 7.52e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C4' ATP A1103 "
        pdb=" C5' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     115.19  110.48    4.71 1.76e+00 3.23e-01 7.18e+00
  ... (remaining 14004 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 6051
       17.32 -    34.64: 200
       34.64 -    51.95: 44
       51.95 -    69.27: 9
       69.27 -    86.59: 4
  Dihedral angle restraints: 6308
    sinusoidal: 2587
      harmonic: 3721
  Sorted by residual:
  dihedral pdb=" CB  CYS A 593 "
           pdb=" SG  CYS A 593 "
           pdb=" SG  CYS C  85 "
           pdb=" CB  CYS C  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.30   61.30     1      1.00e+01 1.00e-02 4.99e+01
  dihedral pdb=" CA  LYS A 884 "
           pdb=" C   LYS A 884 "
           pdb=" N   ASN A 885 "
           pdb=" CA  ASN A 885 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.19   16.81     0      5.00e+00 4.00e-02 1.13e+01
  dihedral pdb=" N   CYS C  85 "
           pdb=" CA  CYS C  85 "
           pdb=" CB  CYS C  85 "
           pdb=" SG  CYS C  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.72  -57.28     3      1.50e+01 4.44e-03 9.43e+00
  ... (remaining 6305 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1384
       0.060 -    0.120: 162
       0.120 -    0.179: 19
       0.179 -    0.239: 1
       0.239 -    0.299: 2
  Chirality restraints: 1568
  Sorted by residual:
  chirality pdb=" C2' ATP A1103 "
            pdb=" C1' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" O2' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.98    0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" C3' ATP A1103 "
            pdb=" C2' ATP A1103 "
            pdb=" C4' ATP A1103 "
            pdb=" O3' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.92    0.29 2.00e-01 2.50e+01 2.06e+00
  chirality pdb=" C4' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" C5' ATP A1103 "
            pdb=" O4' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.73    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 1565 not shown)

  Planarity restraints: 1812
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 118 "   -0.010 2.00e-02 2.50e+03   1.91e-02 3.63e+00
        pdb=" C   GLU A 118 "    0.033 2.00e-02 2.50e+03
        pdb=" O   GLU A 118 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   TYR A 119 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C  75 "   -0.022 5.00e-02 4.00e+02   3.36e-02 1.80e+00
        pdb=" N   PRO C  76 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO C  76 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C  76 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  94 "    0.021 5.00e-02 4.00e+02   3.27e-02 1.71e+00
        pdb=" N   PRO C  95 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1809 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 69
        2.59 -     3.17: 8500
        3.17 -     3.74: 14717
        3.74 -     4.32: 22137
        4.32 -     4.90: 37575
  Nonbonded interactions: 82998
  Sorted by model distance:
  nonbonded pdb="MG    MG A1101 "
            pdb=" O2B ATP A1103 "
     model   vdw
     2.012 2.170
  nonbonded pdb=" OD2 ASP A 465 "
            pdb="MG    MG A1102 "
     model   vdw
     2.044 2.170
  nonbonded pdb=" OD2 ASP A 537 "
            pdb="MG    MG A1101 "
     model   vdw
     2.052 2.170
  nonbonded pdb=" OD2 ASP A 463 "
            pdb=" O3' ATP A1103 "
     model   vdw
     2.098 3.040
  nonbonded pdb=" OD1 ASN D  25 "
            pdb=" NZ  LYS D  29 "
     model   vdw
     2.116 3.120
  ... (remaining 82993 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 1 through 75)
  selection = (chain 'D' and resid 1 through 75)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     26.220
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
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      :  0.004   0.072  10344  Z= 0.225
  Angle     :  0.466   9.478  14009  Z= 0.237
  Chirality :  0.043   0.299   1568
  Planarity :  0.003   0.034   1812
  Dihedral  :  9.737  86.589   3901
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 1.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  3.10 %
    Favored  : 95.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.24), residues: 1273
  helix:  1.66 (0.24), residues: 506
  sheet:  0.78 (0.35), residues: 208
  loop :  0.55 (0.27), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 669 
 HIS   0.003   0.001   HIS C  75 
 PHE   0.011   0.001   PHE A 237 
 TYR   0.008   0.001   TYR A 544 
 ARG   0.003   0.000   ARG A 409 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 154
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7419 (tp30) cc_final: 0.7011 (tp30)
REVERT: A   32 MET cc_start: 0.8377 (mtp) cc_final: 0.8091 (mtp)
REVERT: A   33 LYS cc_start: 0.7993 (ttpt) cc_final: 0.7714 (ttmm)
REVERT: A  184 MET cc_start: 0.8383 (mtp) cc_final: 0.8111 (mtt)
REVERT: A  196 MET cc_start: 0.8952 (mmp) cc_final: 0.8701 (mmp)
REVERT: A  216 LYS cc_start: 0.7147 (mtmm) cc_final: 0.6817 (pttp)
REVERT: A  262 LYS cc_start: 0.8936 (ttpp) cc_final: 0.8735 (tmtt)
REVERT: A  286 MET cc_start: 0.8394 (mmm) cc_final: 0.7830 (pmt)
REVERT: A  448 MET cc_start: 0.8910 (mmp) cc_final: 0.8620 (mmp)
REVERT: A  596 LYS cc_start: 0.8578 (tmtt) cc_final: 0.8374 (mmmm)
REVERT: A  611 ASP cc_start: 0.7233 (m-30) cc_final: 0.7033 (m-30)
REVERT: A  652 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7941 (tmm-80)
REVERT: A  832 MET cc_start: 0.8503 (mtp) cc_final: 0.8250 (mtp)
REVERT: A  869 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7647 (mp0)
REVERT: A  879 LYS cc_start: 0.8723 (mmmm) cc_final: 0.8350 (mmtt)
REVERT: A 1011 LYS cc_start: 0.8666 (ttmm) cc_final: 0.8343 (ttmm)
REVERT: B   51 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8235 (mt-10)
REVERT: B   58 ASP cc_start: 0.8146 (m-30) cc_final: 0.7552 (m-30)
REVERT: C    8 ARG cc_start: 0.7996 (mtt-85) cc_final: 0.7687 (ttp-170)
REVERT: C  136 LEU cc_start: 0.8285 (mm) cc_final: 0.7947 (tp)
REVERT: C  143 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8168 (mtm110)
  outliers start: 12
  outliers final: 5
  residues processed: 164
  average time/residue: 1.5034
  time to fit residues: 262.7790
Evaluate side-chains
  119 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain C residue   59 ASP
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue   91 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 51 optimal weight:    0.3980
   chunk 98 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0770
   chunk 60 optimal weight:    0.8980
   chunk 73 optimal weight:    0.0470
   chunk 114 optimal weight:    0.4980
   overall best weight:    0.3436

-------------------------------------------------------------------------------
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 = 0.3901 r_free = 0.3901 target = 0.150660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.097848 restraints weight = 12737.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 2.53
r_work: 0.2989 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2835 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.1074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10344  Z= 0.170
  Angle     :  0.473   6.698  14009  Z= 0.246
  Chirality :  0.042   0.153   1568
  Planarity :  0.004   0.039   1812
  Dihedral  :  6.085  80.920   1416
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 2.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  8.23 %
    Favored  : 90.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.24), residues: 1273
  helix:  1.78 (0.24), residues: 511
  sheet:  0.97 (0.35), residues: 206
  loop :  0.60 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 669 
 HIS   0.002   0.001   HIS A 458 
 PHE   0.010   0.001   PHE A 842 
 TYR   0.009   0.001   TYR A 736 
 ARG   0.006   0.000   ARG C   5 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7802 (tp30) cc_final: 0.7384 (tp30)
REVERT: A   32 MET cc_start: 0.8549 (mtp) cc_final: 0.8345 (mtp)
REVERT: A   33 LYS cc_start: 0.8321 (ttpt) cc_final: 0.8009 (ttmm)
REVERT: A  184 MET cc_start: 0.8503 (mtp) cc_final: 0.8181 (mtt)
REVERT: A  196 MET cc_start: 0.8995 (mmp) cc_final: 0.8669 (mmp)
REVERT: A  216 LYS cc_start: 0.7237 (mtmm) cc_final: 0.6850 (pttp)
REVERT: A  286 MET cc_start: 0.8928 (mmm) cc_final: 0.8241 (pmt)
REVERT: A  540 GLU cc_start: 0.8313 (tt0) cc_final: 0.8111 (mp0)
REVERT: A  543 MET cc_start: 0.8932 (mmt) cc_final: 0.8671 (mmt)
REVERT: A  841 ARG cc_start: 0.8140 (ttm170) cc_final: 0.7545 (mtp180)
REVERT: A  869 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7901 (mp0)
REVERT: A  879 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8294 (mmtt)
REVERT: A  981 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8176 (mptm)
REVERT: B   11 LYS cc_start: 0.8514 (tttt) cc_final: 0.8153 (tttm)
REVERT: B   51 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8351 (mt-10)
REVERT: B   58 ASP cc_start: 0.8021 (m-30) cc_final: 0.7305 (m-30)
REVERT: C    8 ARG cc_start: 0.8125 (mtt-85) cc_final: 0.7766 (ttp-170)
REVERT: C  135 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.7121 (mp0)
REVERT: C  136 LEU cc_start: 0.8160 (mm) cc_final: 0.7796 (tp)
REVERT: C  143 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8178 (mtm110)
REVERT: C  144 LYS cc_start: 0.8471 (ttmt) cc_final: 0.8153 (ttmt)
REVERT: D    1 MET cc_start: 0.5775 (OUTLIER) cc_final: 0.5446 (mtm)
  outliers start: 18
  outliers final: 7
  residues processed: 132
  average time/residue: 1.4691
  time to fit residues: 207.3374
Evaluate side-chains
  116 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  593 CYS
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  936 LYS
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  111 THR
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain D residue    1 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   chunk 70 optimal weight:    0.0060
   chunk 97 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 101 optimal weight:    3.9990
   overall best weight:    0.4796

-------------------------------------------------------------------------------
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 = 0.3897 r_free = 0.3897 target = 0.150210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.097415 restraints weight = 13003.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 2.55
r_work: 0.2975 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10344  Z= 0.185
  Angle     :  0.453   6.029  14009  Z= 0.237
  Chirality :  0.042   0.156   1568
  Planarity :  0.004   0.045   1812
  Dihedral  :  6.037  84.574   1412
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  8.85 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.24), residues: 1273
  helix:  1.80 (0.24), residues: 511
  sheet:  1.05 (0.35), residues: 206
  loop :  0.62 (0.28), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 669 
 HIS   0.002   0.000   HIS C  75 
 PHE   0.010   0.001   PHE A 237 
 TYR   0.007   0.001   TYR A 736 
 ARG   0.011   0.000   ARG A 645 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7859 (tp30) cc_final: 0.7417 (tp30)
REVERT: A   32 MET cc_start: 0.8550 (mtp) cc_final: 0.8319 (mtp)
REVERT: A   33 LYS cc_start: 0.8409 (ttpt) cc_final: 0.7994 (ttmm)
REVERT: A  184 MET cc_start: 0.8474 (mtp) cc_final: 0.8109 (mtt)
REVERT: A  196 MET cc_start: 0.8992 (mmp) cc_final: 0.8755 (tpp)
REVERT: A  216 LYS cc_start: 0.7276 (mtmm) cc_final: 0.6914 (pttp)
REVERT: A  286 MET cc_start: 0.8907 (mmm) cc_final: 0.8241 (pmt)
REVERT: A  540 GLU cc_start: 0.8359 (tt0) cc_final: 0.8136 (mp0)
REVERT: A  869 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7952 (mp0)
REVERT: A  879 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8346 (mmtt)
REVERT: A  980 LYS cc_start: 0.7976 (ptmt) cc_final: 0.7403 (ptpt)
REVERT: A  981 LYS cc_start: 0.8649 (mtpp) cc_final: 0.8221 (mptm)
REVERT: B   11 LYS cc_start: 0.8473 (tttt) cc_final: 0.8190 (tttm)
REVERT: B   51 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8311 (mt-10)
REVERT: B   58 ASP cc_start: 0.8095 (m-30) cc_final: 0.7400 (m-30)
REVERT: B   71 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8958 (pp)
REVERT: C    8 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7856 (ttp-170)
REVERT: C  135 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.7002 (mp0)
REVERT: C  136 LEU cc_start: 0.8170 (mm) cc_final: 0.7783 (tp)
REVERT: C  143 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8017 (mtm110)
REVERT: D    1 MET cc_start: 0.5785 (OUTLIER) cc_final: 0.5425 (mtm)
  outliers start: 25
  outliers final: 9
  residues processed: 126
  average time/residue: 1.4645
  time to fit residues: 197.1229
Evaluate side-chains
  123 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 1.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  896 THR
Chi-restraints excluded: chain A residue  936 LYS
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain D residue    1 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9980
   chunk 89 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3878 r_free = 0.3878 target = 0.148645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.095781 restraints weight = 12892.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 2.53
r_work: 0.2953 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10344  Z= 0.296
  Angle     :  0.491   7.232  14009  Z= 0.255
  Chirality :  0.044   0.167   1568
  Planarity :  0.004   0.059   1812
  Dihedral  :  6.077  83.321   1411
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  :  9.65 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.24), residues: 1273
  helix:  1.67 (0.24), residues: 510
  sheet:  1.08 (0.35), residues: 211
  loop :  0.58 (0.28), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 669 
 HIS   0.002   0.001   HIS C  75 
 PHE   0.012   0.001   PHE A 237 
 TYR   0.009   0.001   TYR A  81 
 ARG   0.008   0.000   ARG A 645 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7897 (tp30) cc_final: 0.7282 (tp30)
REVERT: A   32 MET cc_start: 0.8581 (mtp) cc_final: 0.8363 (mtp)
REVERT: A   33 LYS cc_start: 0.8406 (ttpt) cc_final: 0.7989 (ttmm)
REVERT: A  184 MET cc_start: 0.8588 (mtp) cc_final: 0.8297 (mtt)
REVERT: A  196 MET cc_start: 0.9009 (mmp) cc_final: 0.8728 (mmp)
REVERT: A  216 LYS cc_start: 0.7302 (mtmm) cc_final: 0.6950 (pttp)
REVERT: A  286 MET cc_start: 0.8909 (mmm) cc_final: 0.8225 (pmt)
REVERT: A  540 GLU cc_start: 0.8391 (tt0) cc_final: 0.8127 (mp0)
REVERT: A  611 ASP cc_start: 0.7737 (m-30) cc_final: 0.7534 (m-30)
REVERT: A  869 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7960 (mp0)
REVERT: A  879 LYS cc_start: 0.8865 (mmmm) cc_final: 0.8361 (mmtt)
REVERT: A  919 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8611 (pmm-80)
REVERT: A  980 LYS cc_start: 0.8015 (ptmt) cc_final: 0.7451 (ptpt)
REVERT: B   11 LYS cc_start: 0.8464 (tttt) cc_final: 0.8204 (tttm)
REVERT: B   51 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8337 (mt-10)
REVERT: B   58 ASP cc_start: 0.8139 (m-30) cc_final: 0.7456 (m-30)
REVERT: B   71 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8933 (pp)
REVERT: C    8 ARG cc_start: 0.8273 (mtt-85) cc_final: 0.7880 (ttp-170)
REVERT: C  135 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7018 (mp0)
REVERT: C  136 LEU cc_start: 0.8131 (mm) cc_final: 0.7767 (tp)
REVERT: C  143 ARG cc_start: 0.8314 (ttp80) cc_final: 0.8005 (mtm110)
REVERT: C  144 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8171 (ttmt)
REVERT: D    1 MET cc_start: 0.5814 (OUTLIER) cc_final: 0.5343 (mtm)
  outliers start: 25
  outliers final: 14
  residues processed: 129
  average time/residue: 1.4635
  time to fit residues: 202.9768
Evaluate side-chains
  131 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 111
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  896 THR
Chi-restraints excluded: chain A residue  919 ARG
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  144 LYS
Chi-restraints excluded: chain D residue    1 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 113 optimal weight:    0.3980
   chunk 27 optimal weight:    0.8980
   chunk 36 optimal weight:    0.3980
   chunk 111 optimal weight:    0.0030
   chunk 96 optimal weight:    0.6980
   chunk 80 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 119 optimal weight:   10.0000
   chunk 52 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.4390

-------------------------------------------------------------------------------
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 = 0.3896 r_free = 0.3896 target = 0.150199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.097492 restraints weight = 12850.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.53
r_work: 0.2983 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10344  Z= 0.177
  Angle     :  0.465   9.174  14009  Z= 0.240
  Chirality :  0.043   0.391   1568
  Planarity :  0.004   0.048   1812
  Dihedral  :  5.945  79.035   1411
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  :  9.82 %
    Favored  : 87.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.24), residues: 1273
  helix:  1.74 (0.24), residues: 510
  sheet:  0.98 (0.34), residues: 214
  loop :  0.56 (0.28), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 669 
 HIS   0.001   0.000   HIS C  75 
 PHE   0.009   0.001   PHE A 237 
 TYR   0.007   0.001   TYR C  74 
 ARG   0.013   0.000   ARG A 645 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7931 (tp30) cc_final: 0.7330 (tp30)
REVERT: A   32 MET cc_start: 0.8549 (mtp) cc_final: 0.8313 (mtp)
REVERT: A   33 LYS cc_start: 0.8402 (ttpt) cc_final: 0.7988 (ttmm)
REVERT: A  184 MET cc_start: 0.8458 (mtp) cc_final: 0.8165 (mtt)
REVERT: A  216 LYS cc_start: 0.7306 (mtmm) cc_final: 0.6960 (pttp)
REVERT: A  286 MET cc_start: 0.8860 (mmm) cc_final: 0.8194 (pmt)
REVERT: A  540 GLU cc_start: 0.8341 (tt0) cc_final: 0.8138 (mp0)
REVERT: A  543 MET cc_start: 0.9021 (mmt) cc_final: 0.8751 (mmp)
REVERT: A  869 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7929 (mp0)
REVERT: A  879 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8344 (mmtt)
REVERT: A  980 LYS cc_start: 0.8001 (ptmt) cc_final: 0.7449 (ptpt)
REVERT: A  981 LYS cc_start: 0.8587 (mtpp) cc_final: 0.8251 (mptm)
REVERT: B   51 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8317 (mt-10)
REVERT: B   58 ASP cc_start: 0.8122 (m-30) cc_final: 0.7391 (m-30)
REVERT: B   71 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8955 (pp)
REVERT: C    8 ARG cc_start: 0.8286 (mtt-85) cc_final: 0.7896 (ttp-170)
REVERT: C  135 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7068 (mp0)
REVERT: C  136 LEU cc_start: 0.8123 (mm) cc_final: 0.7757 (tp)
REVERT: C  143 ARG cc_start: 0.8311 (ttp80) cc_final: 0.7983 (mtm110)
REVERT: D    1 MET cc_start: 0.5728 (OUTLIER) cc_final: 0.5288 (mtm)
  outliers start: 27
  outliers final: 14
  residues processed: 118
  average time/residue: 1.3615
  time to fit residues: 172.8062
Evaluate side-chains
  113 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 1.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  896 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  144 LYS
Chi-restraints excluded: chain D residue    1 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 83 optimal weight:    0.5980
   chunk 101 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 53 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3877 r_free = 0.3877 target = 0.148677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.095968 restraints weight = 12974.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3113 rms_B_bonded: 2.53
r_work: 0.2957 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10344  Z= 0.269
  Angle     :  0.481   8.057  14009  Z= 0.249
  Chirality :  0.043   0.163   1568
  Planarity :  0.004   0.049   1812
  Dihedral  :  6.021  75.957   1411
  Min Nonbonded Distance : 1.925

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.35 %
    Favored  : 87.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.24), residues: 1273
  helix:  1.69 (0.24), residues: 510
  sheet:  0.96 (0.34), residues: 222
  loop :  0.57 (0.28), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 669 
 HIS   0.002   0.001   HIS C  75 
 PHE   0.014   0.001   PHE A 237 
 TYR   0.009   0.001   TYR A 544 
 ARG   0.011   0.000   ARG A 645 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7958 (tp30) cc_final: 0.7431 (tp30)
REVERT: A   32 MET cc_start: 0.8552 (mtp) cc_final: 0.8295 (mtp)
REVERT: A   33 LYS cc_start: 0.8418 (ttpt) cc_final: 0.7981 (ttmm)
REVERT: A  184 MET cc_start: 0.8563 (mtp) cc_final: 0.8338 (mtt)
REVERT: A  196 MET cc_start: 0.8899 (tpp) cc_final: 0.8566 (mmp)
REVERT: A  216 LYS cc_start: 0.7355 (mtmm) cc_final: 0.6991 (pttp)
REVERT: A  286 MET cc_start: 0.8875 (mmm) cc_final: 0.8218 (pmt)
REVERT: A  540 GLU cc_start: 0.8378 (tt0) cc_final: 0.8104 (mp0)
REVERT: A  543 MET cc_start: 0.9020 (mmt) cc_final: 0.8795 (mmt)
REVERT: A  869 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7960 (mp0)
REVERT: A  879 LYS cc_start: 0.8856 (mmmm) cc_final: 0.8343 (mmtt)
REVERT: A  980 LYS cc_start: 0.8080 (ptmt) cc_final: 0.7497 (ptpt)
REVERT: A  981 LYS cc_start: 0.8620 (mtpp) cc_final: 0.8241 (mptm)
REVERT: B   11 LYS cc_start: 0.8464 (tttt) cc_final: 0.8229 (tttm)
REVERT: B   58 ASP cc_start: 0.8148 (m-30) cc_final: 0.7408 (m-30)
REVERT: B   71 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8949 (pp)
REVERT: C    8 ARG cc_start: 0.8267 (mtt-85) cc_final: 0.7958 (ttp-170)
REVERT: C  135 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7072 (mp0)
REVERT: C  136 LEU cc_start: 0.8088 (mm) cc_final: 0.7725 (tp)
REVERT: C  143 ARG cc_start: 0.8300 (ttp80) cc_final: 0.8001 (mtm110)
REVERT: D    1 MET cc_start: 0.5845 (mtm) cc_final: 0.5448 (mtm)
  outliers start: 24
  outliers final: 13
  residues processed: 113
  average time/residue: 1.4344
  time to fit residues: 173.5807
Evaluate side-chains
  123 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  896 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  144 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    0.2980
   chunk 79 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.149457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.096625 restraints weight = 12978.850|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 2.53
r_work: 0.2971 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10344  Z= 0.218
  Angle     :  0.470  10.730  14009  Z= 0.243
  Chirality :  0.043   0.329   1568
  Planarity :  0.004   0.049   1812
  Dihedral  :  5.942  74.597   1411
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 2.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 10.27 %
    Favored  : 87.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.24), residues: 1273
  helix:  1.69 (0.24), residues: 510
  sheet:  0.92 (0.34), residues: 217
  loop :  0.57 (0.28), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 669 
 HIS   0.002   0.001   HIS C  75 
 PHE   0.012   0.001   PHE A 237 
 TYR   0.007   0.001   TYR A  81 
 ARG   0.008   0.000   ARG A 645 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7973 (tp30) cc_final: 0.7377 (tp30)
REVERT: A   32 MET cc_start: 0.8535 (mtp) cc_final: 0.8256 (mtp)
REVERT: A   33 LYS cc_start: 0.8417 (ttpt) cc_final: 0.7986 (ttmm)
REVERT: A  184 MET cc_start: 0.8494 (mtp) cc_final: 0.8224 (mtt)
REVERT: A  196 MET cc_start: 0.8893 (tpp) cc_final: 0.8526 (mmp)
REVERT: A  216 LYS cc_start: 0.7361 (mtmm) cc_final: 0.7005 (pttp)
REVERT: A  286 MET cc_start: 0.8836 (mmm) cc_final: 0.8183 (pmt)
REVERT: A  540 GLU cc_start: 0.8362 (tt0) cc_final: 0.8131 (mp0)
REVERT: A  543 MET cc_start: 0.8986 (mmt) cc_final: 0.8772 (mmt)
REVERT: A  869 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7938 (mp0)
REVERT: A  879 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8326 (mmtt)
REVERT: A  980 LYS cc_start: 0.8099 (ptmt) cc_final: 0.7486 (ptpt)
REVERT: A  981 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8249 (mptm)
REVERT: B   71 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8943 (pp)
REVERT: C    8 ARG cc_start: 0.8272 (mtt-85) cc_final: 0.7967 (ttp-170)
REVERT: C  135 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.7062 (mp0)
REVERT: C  136 LEU cc_start: 0.8121 (mm) cc_final: 0.7751 (tp)
REVERT: C  143 ARG cc_start: 0.8328 (ttp80) cc_final: 0.8023 (mtm110)
REVERT: D    1 MET cc_start: 0.5833 (OUTLIER) cc_final: 0.5408 (mtm)
  outliers start: 27
  outliers final: 14
  residues processed: 124
  average time/residue: 1.3767
  time to fit residues: 183.0040
Evaluate side-chains
  124 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  896 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  144 LYS
Chi-restraints excluded: chain D residue    1 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 108 optimal weight:    0.7980
   chunk 119 optimal weight:    9.9990
   chunk 125 optimal weight:    7.9990
   chunk 58 optimal weight:    0.4980
   chunk 72 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 118 optimal weight:    0.5980
   chunk 121 optimal weight:    5.9990
   chunk 42 optimal weight:    0.5980
   chunk 68 optimal weight:    0.0570
   overall best weight:    0.4898

-------------------------------------------------------------------------------
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 = 0.3847 r_free = 0.3847 target = 0.147240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.093913 restraints weight = 13045.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 2.54
r_work: 0.2976 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10344  Z= 0.185
  Angle     :  0.464   8.852  14009  Z= 0.241
  Chirality :  0.042   0.200   1568
  Planarity :  0.004   0.048   1812
  Dihedral  :  5.914  75.357   1411
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.71 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.24), residues: 1273
  helix:  1.70 (0.24), residues: 510
  sheet:  0.93 (0.34), residues: 217
  loop :  0.60 (0.28), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 669 
 HIS   0.002   0.000   HIS C  32 
 PHE   0.011   0.001   PHE A 237 
 TYR   0.007   0.001   TYR C  74 
 ARG   0.007   0.000   ARG A 645 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7966 (tp30) cc_final: 0.7365 (tp30)
REVERT: A   32 MET cc_start: 0.8544 (mtp) cc_final: 0.8342 (mtp)
REVERT: A   33 LYS cc_start: 0.8427 (ttpt) cc_final: 0.7998 (ttmm)
REVERT: A  184 MET cc_start: 0.8457 (mtp) cc_final: 0.8155 (mtt)
REVERT: A  196 MET cc_start: 0.8871 (tpp) cc_final: 0.8483 (mmp)
REVERT: A  216 LYS cc_start: 0.7370 (mtmm) cc_final: 0.7012 (pttp)
REVERT: A  286 MET cc_start: 0.8835 (mmm) cc_final: 0.8193 (pmt)
REVERT: A  540 GLU cc_start: 0.8363 (tt0) cc_final: 0.8137 (mp0)
REVERT: A  869 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7929 (mp0)
REVERT: A  879 LYS cc_start: 0.8832 (mmmm) cc_final: 0.8315 (mmtt)
REVERT: A  980 LYS cc_start: 0.8101 (ptmt) cc_final: 0.7484 (ptpt)
REVERT: A  981 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8249 (mptm)
REVERT: B   71 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8940 (pp)
REVERT: C    8 ARG cc_start: 0.8277 (mtt-85) cc_final: 0.7980 (ttp-170)
REVERT: C  135 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.7087 (mp0)
REVERT: C  136 LEU cc_start: 0.8137 (mm) cc_final: 0.7766 (tp)
REVERT: C  143 ARG cc_start: 0.8338 (ttp80) cc_final: 0.8016 (mtm110)
REVERT: D    1 MET cc_start: 0.5787 (OUTLIER) cc_final: 0.5354 (mtm)
  outliers start: 24
  outliers final: 16
  residues processed: 113
  average time/residue: 1.4416
  time to fit residues: 175.1344
Evaluate side-chains
  118 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  448 MET
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  896 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  144 LYS
Chi-restraints excluded: chain D residue    1 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 112 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0570
   chunk 8 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   overall best weight:    0.8098

-------------------------------------------------------------------------------
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 = 0.3835 r_free = 0.3835 target = 0.146231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.092781 restraints weight = 13062.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.53
r_work: 0.2961 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10344  Z= 0.272
  Angle     :  0.522  12.966  14009  Z= 0.268
  Chirality :  0.044   0.316   1568
  Planarity :  0.004   0.051   1812
  Dihedral  :  5.882  79.102   1410
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 11.15 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.24), residues: 1273
  helix:  1.60 (0.23), residues: 510
  sheet:  0.95 (0.33), residues: 222
  loop :  0.55 (0.28), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 669 
 HIS   0.002   0.001   HIS C  75 
 PHE   0.013   0.001   PHE A 237 
 TYR   0.009   0.001   TYR A 544 
 ARG   0.006   0.000   ARG A 645 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.7997 (tp30) cc_final: 0.7471 (tp30)
REVERT: A   32 MET cc_start: 0.8569 (mtp) cc_final: 0.8344 (mtp)
REVERT: A   33 LYS cc_start: 0.8444 (ttpt) cc_final: 0.7997 (ttmm)
REVERT: A  184 MET cc_start: 0.8453 (mtp) cc_final: 0.8194 (mtt)
REVERT: A  216 LYS cc_start: 0.7350 (mtmm) cc_final: 0.7019 (pttp)
REVERT: A  286 MET cc_start: 0.8857 (mmm) cc_final: 0.8205 (pmt)
REVERT: A  540 GLU cc_start: 0.8391 (tt0) cc_final: 0.8139 (mp0)
REVERT: A  543 MET cc_start: 0.9030 (mmt) cc_final: 0.8751 (mmp)
REVERT: A  869 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7960 (mp0)
REVERT: A  879 LYS cc_start: 0.8848 (mmmm) cc_final: 0.8331 (mmtt)
REVERT: A  980 LYS cc_start: 0.8123 (ptmt) cc_final: 0.7502 (ptpt)
REVERT: A  981 LYS cc_start: 0.8622 (mtpp) cc_final: 0.8236 (mptm)
REVERT: B   11 LYS cc_start: 0.8494 (tttt) cc_final: 0.8244 (tttm)
REVERT: B   71 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8951 (pp)
REVERT: C    8 ARG cc_start: 0.8271 (mtt-85) cc_final: 0.7972 (ttp-170)
REVERT: C  135 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7109 (mp0)
REVERT: C  136 LEU cc_start: 0.8151 (mm) cc_final: 0.7779 (tp)
REVERT: C  143 ARG cc_start: 0.8325 (ttp80) cc_final: 0.8011 (mtm110)
REVERT: D    1 MET cc_start: 0.5749 (mtm) cc_final: 0.5296 (mtm)
  outliers start: 22
  outliers final: 15
  residues processed: 113
  average time/residue: 1.4399
  time to fit residues: 174.1982
Evaluate side-chains
  121 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  896 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  144 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 97 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 117 optimal weight:    0.1980
   chunk 42 optimal weight:    0.5980
   chunk 112 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3882 r_free = 0.3882 target = 0.149218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.096498 restraints weight = 12991.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 2.53
r_work: 0.2963 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10344  Z= 0.220
  Angle     :  0.504  11.717  14009  Z= 0.260
  Chirality :  0.043   0.191   1568
  Planarity :  0.004   0.054   1812
  Dihedral  :  5.832  76.708   1410
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.15 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.24), residues: 1273
  helix:  1.59 (0.23), residues: 510
  sheet:  0.96 (0.34), residues: 222
  loop :  0.56 (0.28), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 669 
 HIS   0.002   0.001   HIS C  75 
 PHE   0.012   0.001   PHE A 237 
 TYR   0.008   0.001   TYR A 544 
 ARG   0.006   0.000   ARG A 645 

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 1.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8005 (tp30) cc_final: 0.7347 (tp30)
REVERT: A   32 MET cc_start: 0.8557 (mtp) cc_final: 0.8337 (mtp)
REVERT: A   33 LYS cc_start: 0.8448 (ttpt) cc_final: 0.8015 (ttmm)
REVERT: A  184 MET cc_start: 0.8437 (mtp) cc_final: 0.8180 (mtt)
REVERT: A  196 MET cc_start: 0.8809 (tpp) cc_final: 0.8506 (mmp)
REVERT: A  216 LYS cc_start: 0.7360 (mtmm) cc_final: 0.7035 (pttp)
REVERT: A  286 MET cc_start: 0.8848 (mmm) cc_final: 0.8210 (pmt)
REVERT: A  540 GLU cc_start: 0.8381 (tt0) cc_final: 0.8141 (mp0)
REVERT: A  543 MET cc_start: 0.9021 (mmt) cc_final: 0.8750 (mmp)
REVERT: A  869 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7929 (mp0)
REVERT: A  879 LYS cc_start: 0.8841 (mmmm) cc_final: 0.8327 (mmtt)
REVERT: A  980 LYS cc_start: 0.8129 (ptmt) cc_final: 0.7513 (ptpt)
REVERT: A  981 LYS cc_start: 0.8624 (mtpp) cc_final: 0.8241 (mptm)
REVERT: B   71 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8943 (pp)
REVERT: C    8 ARG cc_start: 0.8282 (mtt-85) cc_final: 0.7982 (ttp-170)
REVERT: C  135 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7127 (mp0)
REVERT: C  136 LEU cc_start: 0.8173 (mm) cc_final: 0.7803 (tp)
REVERT: C  143 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8019 (mtm110)
REVERT: D    1 MET cc_start: 0.5646 (mtm) cc_final: 0.5181 (mtm)
  outliers start: 21
  outliers final: 16
  residues processed: 118
  average time/residue: 1.3643
  time to fit residues: 172.7030
Evaluate side-chains
  113 residues out of total 1130 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LYS
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  582 SER
Chi-restraints excluded: chain A residue  656 VAL
Chi-restraints excluded: chain A residue  710 THR
Chi-restraints excluded: chain A residue  855 MET
Chi-restraints excluded: chain A residue  869 GLU
Chi-restraints excluded: chain A residue  896 THR
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   28 SER
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain C residue   91 ASP
Chi-restraints excluded: chain C residue  110 LEU
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  144 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0770
   chunk 123 optimal weight:    8.9990
   chunk 105 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 38 optimal weight:    0.0970
   chunk 52 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   overall best weight:    0.4136

-------------------------------------------------------------------------------
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 = 0.3893 r_free = 0.3893 target = 0.150145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.097583 restraints weight = 12899.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 2.53
r_work: 0.2981 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10344  Z= 0.171
  Angle     :  0.493  10.778  14009  Z= 0.254
  Chirality :  0.042   0.241   1568
  Planarity :  0.004   0.058   1812
  Dihedral  :  5.709  71.624   1410
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.59 %
    Favored  : 86.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.35 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.24), residues: 1273
  helix:  1.66 (0.24), residues: 510
  sheet:  1.03 (0.34), residues: 222
  loop :  0.59 (0.28), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 669 
 HIS   0.002   0.000   HIS C  32 
 PHE   0.010   0.001   PHE A 237 
 TYR   0.007   0.001   TYR C  74 
 ARG   0.010   0.000   ARG A 645 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 8221.86 seconds
wall clock time: 145 minutes 36.28 seconds (8736.28 seconds total)